[ccp4bb] Number of Molecules in Asymetric Unit
Dear CCP4 Community ,which program i should use in ccp4 backage to find how many molecules in Asymetric Unit .All the bestAmr
[ccp4bb] Formulation of my own mother liquor
Dear All,first i wish you nice weekend, then i wanna ask about formulation of my own mother liquor, i want to optimize a condition containing 0.2m MgCl2, 0.1m Tris , PH 8; and 20% PEG6K as pricipitant. (PACT)the question is , should i make a stock solution from every ingredient by dissolving it in miliQ water. then mix all stuff together and add water till final concentration with out adjusting final pH. OR dissolve the PEG in pH adjusted buffer and then mix all ingredients , so the final pH will be 8.any suggest any idea or any one knows what the company do. CHEERSAmr
[ccp4bb] Adding zink and coper by COOT
Dear ccp4bb Community ,i hope this email finds you well, i am trying to do add Zink and Copper to my Superoxid dismuase Enzyme by Coot , i encountered two problems.1- after adding Zink and copper by place atom at pointer other writing ZN OR CU then running Refmac5 , both atom is turned to water 2- i traied to added atom and merge the atoms with coordinate file out side the coot. the atoms are added but i see red patches arround them. i also added calcium instead then i replaced them bz editing the PDB file.3- the Rfactor 16 and R free is 22.1 so my questionhow can i add zink and copper in right way. second what is the red patches mean?thank you in advance Amr
Re: [ccp4bb] amro selem
http://www.alliancecorporation.com/gtjxdgki/dqtyk/psx/ycqd/uuens/fdcl/opzb.htm Best regards, amro selem
[ccp4bb] Factor 10a
Dear colleagues, i hope every one doing well. i am trying to remove the 10x his tag , as i tried to crystallize with the tag but i didn^t obtain crystals unless some salt crystals , very small crystals and some precipitant. i want to use factor 10a protease but i didn^t tried it before. this is the first time for using it. i have factor 10a protease from Qiagen 400 unit . i have read the protocol but i still need some suggestion and experience as you know it is expensive. also i have another question , how many protein digested by one unit ? i know it depend but roughly how much? i really appreciate your support. best regards Amr
[ccp4bb] Factor 10a protease
Dear colleagues, i hope every one doing well. i am trying to remove the 10x his tag , as i tried to crystallize with the tag but i didn^t obtain crystals unless some salt crystals , very small crystals and some precipitant. i want to use factor 10a protease but i didn^t tried it before. this is the first time for using it. i have factor 10a protease from Qiagen 400 unit . i have read the protocol but i still need some suggestion and experience as you know it is expensive. also i have another question , how many protein digested by one unit ? i know it depend but roughly how much? i really appreciate your support. best regards Amr
[ccp4bb] sequencing
Dear all , my job is to clone part of the gene already carried on pJC40 vector .i sent this vector for sequencing . i made also squence alignment, i have found only 97% identity . this mean about five nuclutides are not matching with original sequence . when i made protein blast i also found 4 amino acid were altered . this is sequencing result 10285313.seq - ID: 130912 Amr-T7 on 2012/9/17-4:14:28 automatically edited with PhredPhrap, start with base no.: 10 Internal Params: Windowsize: 20, Goodqual: 19, Badqual: 10, Minseqlength: 50, nbadelimit: 1 tnaaaTaTTTtgTTTtaCTTtAGanngagaTATACCatggGGcCATCATCATCATCATCATCATCATCATCACAGCAGCGGCCATATCGAAgGTCGTCATATGATAAAcgtCGCCAACAACAACAACAACAACAACAGCAACAACAACgtGatgAACGTgGAATACCACCACGGAAGgtGCACCACCAAgtgTTATCGATGAAATAATTTGCTACTGATGTCTGATCAACAAACtgAAGCTGATGTTGAAGCATTCATCAATAGACTTGGTGGCAGTTACAAGGTTCGATTTACTCAATTCATGGAAGAAGTAAAGAAAGCTAGAGCTGATTATGAAAGAATCCATCAGCAGGCAGTAGCAAGACGCCAGCAGCGATGCTGACGCAAGGATGTCCGCTATTGCTGGTTCGCCGCATCTAACTACGCGACATCGCAGCAAATTCAAGCCATCATGGATTCATTATCTGAGAGCGTTCGAGGagaGATCATTAAGGCATTGAGCCCACAAGAATAAGGATCCCGGGCCCTAGCTAACTGATCCGGCTGCTAACAAAGCCCGAAAGGAAGCTGAGTTGGCTGCTGCCACCGCTGAGCAATAACTAGCATAATTCCTCTAAACGGGTCTTGATTGCTGAAAGGAGGAACTATATCCGGATAATTCTTGAAGACGAAAGGGCCTCGTGATACGCCTATtTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACCAAATGTGCGCGGAACCcCTATTTGTTTATCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAaGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCC this is DNA alignment. gb|U00693.1|OVU00693 Onchocerca volvulus Rainforest immunodominant hypodermal antigen mRNA, complete cds Length=880 Score = 798 bits (432), Expect = 0.0 Identities = 442/447 (99%), Gaps = 0/447 (0%) Strand=Plus/Plus Query 48 ATAAACGTCGCcaacaacaacaacaacaacaacagcaacaacaacGTGATGAACGT 107 Sbjct 117 ATAAACGTCGCCAACAACAACAACAACAACAACAGCAACAACAACGTGATGAACGT 176 Query 108 GGAATACCACCACGGAAGGTGCACCACCAAGTGTTATCGATGAAATAATTTG 167 | || ||| Sbjct 177 GAAATACCACCATGGAAGGTGCACCACCAAGTGTTATCGATGAAATAATTTG 236 Query 168 CTACTGATGTCTGATCAACAAACTGAAGCTGATGTTGAAGCATTCATC 227 Sbjct 237 CTACTGATGTCTGATCAACAAACTGAAGCTGATGTTGAAGCATTCATC 296 Query 228 AATAGACTTGGTGGCAGTTACAAGGTTCGATTTACTCAATTCATGGAAGAAGTAAAGAAA 287 Sbjct 297 AATAGACTTGGTGGCAGTTACAAGGTTCGATTTACTCAATTCATGGAAGAAGTAAAGAAA 356 Query 288 GCTAGAGCTGATTATGAAAGAATCCATCAGCAGGCAGTAGCAAGACGCCAGCAGCA 347 Sbjct 357 GCTAGAGCTGATTATGAAAGAATCCATCAGCAGGCAGTAGCAAGACGCCAGCAGCA 416 Query 348 AAAGATGCTGACGCAAGGATGTCCGCTATTGCTGGTTCGCCGCATCTAACTACGCGACAA 407 || | Sbjct 417 AAAGATGCTGACGCAAGGATGTCCGCTATTGCTGATTCGCCGCATCTAACTACGCGACAA 476 Query 408 AAATCGCAGCAAATTCAAGCCATCATGGATTCATTATCTGAGAGCGTTCGAGGAGAGATC 467 ||| Sbjct 477 AAATCGCAGCAAATTCAAGCCATCATGGATTCATTATCTGAGAGCGTTCGAAGAGAGATC 536 Query 468 ATTAAGGCATTGAGCCCACAAGAATAA 494 | | Sbjct 537 ATTAATGCATTGAGCCCACAAGAATAA 563 and this is amino acid sequence alignment . lcl|8325 unnamed protein product Length=148 Score = 256 bits (655), Expect = 7e-93, Method: Compositional matrix adjust. Identities = 143/148 (97%), Positives = 143/148 (97%), Gaps = 0/148 (0%) Query 1 IPQRRQQQRDEREIPPFLEGAPPSVIDEFYNLLKTDENKTDQQTEADVEAFI 60 IPQRRQQQRDER IPPF EGAPPSVIDEFYNLLKTDENKTDQQTEADVEAFI Sbjct 1 IPQRRQQQRDERGIPPFSEGAPPSVIDEFYNLLKTDENKTDQQTEADVEAFI 60 Query 61 NRLGGSYKVRFTQFMEEVKKARADYERIHQQAVARFSPAAKDADARMSAIADSPHLTTRQ 120 NRLGGSYKVRFTQFMEEVKKARADYERIHQQAVARFSPAAKDADARMSAIA SPHLTTRQ Sbjct 61 NRLGGSYKVRFTQFMEEVKKARADYERIHQQAVARFSPAAKDADARMSAIAGSPHLTTRQ 120 Query 121 KSQQIQAIMDSLSESVRREIINALSPQE 148 KSQQIQAIMDSLSESVR EII ALSPQE Sbjct 121 KSQQIQAIMDSLSESVRGEIIKALSPQE 148. now what should i do? continue and design primers or repeat the sequencing again or begin every thing from zero point . best regards Amr
[ccp4bb] structural homology
Dear all, i want to do structural homology but i am still beginner , could some one help me to do it.is there are specific programs to do that or should i do it manually ? thank you Amr
[ccp4bb] sulphur bridge
Hallo every one, i am working on one enzyme who has sulphur bridge , is using 2 mercaptoethnol or DTT during handling this protein for crystallography is not desirable . best regards Amr
[ccp4bb] hallo every body
hallo every body, i face problem with protein when i make gel filtration or concentrate my protein . i notice sever aggregation . i use only glycerol as additives to 50 mM TRIS and 150 mM NaCL ; PH 8 . my IP is 7.8 . any suggestions. best regards Amr
[ccp4bb] hi all
Hi all , thank you for being new member in this group. i also just stated with my PhD in structural biology at Hamburg University (DESY) . i have no Idea about crystallography . I just go step by step. so please help me to find my way for excellence in structural biology. i appreciate your suggestion like books, review articles, advices,lectures, power point presentation but more simple . thanks a lot for reading yours Amr
