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Crystal structure of 8ANC195 Fab in complex with gp120 of 93TH057 HIV-1 and soluble CD4 D1D2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P9M 4P9M, 3LQA experimental model PDB 3LQA 4P9M, 3LQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.3 298 PEG 3350, HEPES, benzamidine
Crystal Properties Matthews coefficient Solvent content 2.83 56.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.529 α = 90 b = 132.492 β = 90 c = 142.769 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.033 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.9 39.22 98.9 0.133 0.06 9.7 6.4 36730
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) 2.99 3.17 93.9 0.656 2.1 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4P9M, 3LQA 3 39.22 1.33 25931 1412 99.8 0.237 0.235 0.2427 0.272 0.2758 66.79
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 f_dihedral_angle_d 13.454 f_angle_d 1.105 f_chiral_restr 0.049 f_bond_d 0.02 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6963 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 408
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction PHASER phasing Aimless data scaling