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Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 gp120 core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1M MOPS pH 7.5, ).1M Magnesium acetate hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.562 α = 90 b = 68.567 β = 111.36 c = 119.356 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 MARMOSAIC 325 mm CCD 2016-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.979 SSRL BL14-1
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 2.38 50 100 0.16 9.7 3.6 38617
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 2.38 2.43 99 0.908 1.2 2.9
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 3NGB 2.4 37.33 35668 1881 99.65 0.21574 0.21347 0.2173 0.25763 0.2592 RANDOM 44.972
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] -0.74 -0.03 -0.76 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 20.597 r_dihedral_angle_3_deg 18.851 r_dihedral_angle_1_deg 8.87 r_long_range_B_refined 6.886 r_long_range_B_other 6.876 r_scangle_other 2.357 r_angle_refined_deg 1.937 r_mcangle_it 1.611 r_mcangle_other 1.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 20.597 r_dihedral_angle_3_deg 18.851 r_dihedral_angle_1_deg 8.87 r_long_range_B_refined 6.886 r_long_range_B_other 6.876 r_scangle_other 2.357 r_angle_refined_deg 1.937 r_mcangle_it 1.611 r_mcangle_other 1.611 r_scbond_it 1.353 r_scbond_other 1.352 r_angle_other_deg 1.097 r_mcbond_other 0.935 r_mcbond_it 0.934 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5893 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing