What parameters do you refine? Atomic coordinates xy, z The temperature factor of each atom, b Can also refine the occupancy b=8T2x u 2= mean square atomic displacement b results from atomic vibrations and disorder units=82 Example: b=20->0.5a displacement B=80-->1A displ aceme ent
What parameters do you refine? • Atomic coordinates X, Y, Z • The temperature factor of each atom, B • Can also refine the occupancy u B = 8 π2 x u2 2 = mean square atomic displacement B results from atomic vibrations and disorder units = Å2 Example: B = 20 --> 0.5Å displacement B = 80 --> 1Å displacement
Atomic coordinates in the pdb file OCC B ATOI 1 N GLU 28.4923.21223.4651.0070.88 ATOM 2 CA GLU 27.5524.35423.6291.0069.99 ATO 3 C GLU 26.5454.43222.4890.0067.56 ATON 40 GLU 26.9154.25021.3280.0068.09 ATOM 5 CB GLU 28.3265.68323.6800.0072.34 ATOM 6 CG GLU 27.4476.91023.9730.0075.98 ATOM 7 CD GLU 28.1238.24723.6590.0078.43 ATON 8 OE1 GLU 29.3758.29923.6040.0079.32 ATOM 9 OE2 GLU 27.3939.25123.4680.0079.58 ATOM 10 N ARG 25.2744.61022.8521.0063.77 ATOM 11 CA ARG 24.1794.80721.9071.0059.83 ATOM 12 C ARG 23.4113.69821.2191.0056.20 ATOM 13 O ARG 4444444445555555 23.9872.80820.5961.0057.33 ATOM 14 CB ARG 24.6045.78420.8121.0060.86 ATOM 15 CG ARG 23.9267.12720.8661.0061.89 ATOM 16 CD ARG 24.2957.94419.6471.0062.21
Atomic coordinates in the PDB file X Y Z occ B ATOM 1 N GLU 4 28.492 3.212 23.465 1.00 70.88 ATOM 2 CA GLU 4 27.552 4.354 23.629 1.00 69.99 ATOM 3 C GLU 4 26.545 4.432 22.489 0.00 67.56 ATOM 4 O GLU 4 26.915 4.250 21.328 0.00 68.09 ATOM 5 CB GLU 4 28.326 5.683 23.680 0.00 72.34 ATOM 6 CG GLU 4 27.447 6.910 23.973 0.00 75.98 ATOM 7 CD GLU 4 28.123 8.247 23.659 0.00 78.43 ATOM 8 OE1 GLU 4 29.375 8.299 23.604 0.00 79.32 ATOM 9 OE2 GLU 4 27.393 9.251 23.468 0.00 79.58 ATOM 10 N ARG 5 25.274 4.610 22.852 1.00 63.77 ATOM 11 CA ARG 5 24.179 4.807 21.907 1.00 59.83 ATOM 12 C ARG 5 23.411 3.698 21.219 1.00 56.20 ATOM 13 O ARG 5 23.987 2.808 20.596 1.00 57.33 ATOM 14 CB ARG 5 24.604 5.784 20.812 1.00 60.86 ATOM 15 CG ARG 5 23.926 7.127 20.866 1.00 61.89 ATOM 16 CD ARG 5 24.295 7.944 19.647 1.00 62.21
Is your structure correct? How unusual is the structure geometry? ·Doesⅰ t contain rare conformations? Does it make chemical sense? PDB AD ?》◆e PROTEIN DATA BANK Validation Tutorial PDB Home Contact Server The ADIT Validation Server allows the user allows the user to check the format consistency of coordinates (PRECHECk) and to create validation reports about a stucture before depositon (VALIDATION). These checks can be done independently by the user Tutorial I File Format Information I Possible Format Problems I Validation Server at osaka University, Japan I To start a new validation session, select the experimental method (x-ray or NMR) from the pull-down menus below, and press the begiN button Meo:xry÷BE http://pdb.rutgersedu/validate/
Is your structure correct? • How unusual is the structure geometry? • Does it contain rare conformations? • Does it make chemical sense? http://pdb.rutgers.edu/validate/
PROCHECK Backbone geometry Ramachandran plot new-entry R Peptide torsion angles 益 Plot basics Ably № mber d nom gi:nm同Md ber daytime Tesidues showm as1Tamgles) oia nabbed residu http://pdb.rutgersedu w tatty_oLta
Backbone geometry http://pdb.rutgers.edu/
Side chain lle chil distribution geometry x angle here might indicate error in structure 0389 150180210240270300330380 x1 lle chi2 distribution X2 isoleucine www.fCcc.edu/research/labs/dunbrack/confanalysis.html
Side chain geometry O N χ1 χ2 isoleucine χ angle here might www.fccc.edu/research/labs/dunbrack/confanalysis.html indicate error in structure