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Structure of Fab 7D11 from a neutralizing antibody against the poxvirus L1 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YPY 1YPY, 1YMH experimental model PDB 1YMH 1YPY, 1YMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 298 10% PEG 10000, 0.1M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 3.2 61.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.77 α = 90 b = 85.561 β = 119.6 c = 211.843 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2005-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.1 50 98.6 0.124 7 3.3 61289
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 99.6 0.464 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1YPY, 1YMH 3.1 50 61228 3109 98.4 0.24 0.24 0.2366 0.259 0.2548 RANDOM 39.19
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 2.654 c_mcangle_it 2.131 c_scbond_it 1.64 c_angle_deg 1.4 c_mcbond_it 1.189 c_improper_angle_d 0.91 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 2.654 c_mcangle_it 2.131 c_scbond_it 1.64 c_angle_deg 1.4 c_mcbond_it 1.189 c_improper_angle_d 0.91 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18612 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction