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Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.93 295 0.07 M sodium acetate, 30% (v/v) glycerol, 6% (w/v) PEG 4000, pH 3.93
Crystal Properties Matthews coefficient Solvent content 4.05 69.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.59 α = 90 b = 127.59 β = 90 c = 315.507 γ = 120
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 PILATUS3 6M 2016-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03315 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 3.9 50 89 0.15 0.04 0.95 15.7 17.5 23583
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.04 61.7 1.07 0.28 0.7 12.3
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 5CEZ 3.9 50.01 22323 1193 88.87 0.24979 0.24742 0.249 0.29605 0.2941 RANDOM 247.532
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] 8.64 4.32 8.64 -28.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_long_range_B_refined 18.464 r_long_range_B_other 18.463 r_dihedral_angle_4_deg 14.344 r_dihedral_angle_3_deg 13.227 r_mcangle_it 12.938 r_mcangle_other 12.937 r_scangle_other 11.382 r_mcbond_it 7.614 r_mcbond_other 7.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_long_range_B_refined 18.464 r_long_range_B_other 18.463 r_dihedral_angle_4_deg 14.344 r_dihedral_angle_3_deg 13.227 r_mcangle_it 12.938 r_mcangle_other 12.937 r_scangle_other 11.382 r_mcbond_it 7.614 r_mcbond_other 7.614 r_scbond_it 6.439 r_scbond_other 6.437 r_dihedral_angle_1_deg 5.73 r_angle_other_deg 3.825 r_angle_refined_deg 1.32 r_chiral_restr 0.132 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 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 11221 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 625
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing