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Crystal structure of an HIV-1 gp120 engineered outer domain with a Man9 glycan at position N276, in complex with broadly neutralizing antibody VRC01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGB 3NGB and 4JPJ experimental model PDB 4JPJ 3NGB and 4JPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.16 M ammonium sulfate, 20% (w/v) PEG4000, 20% (v/v) glycerol, 0.08 M sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.21 61.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.51 α = 90 b = 113.51 β = 90 c = 412.52 γ = 90
Symmetry Space Group P 41 21 2
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 300 mm CCD 2013-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03324 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.25 40 99.9 0.16 0.995 10.9 8 43730
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.35 100 0.85 0.572 2.2 8.2
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 FREE R-VALUE 3NGB and 4JPJ 3.25 39.943 0.73 43597 2180 99.92 0.2253 0.2228 0.2291 0.2737 0.2734
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 14.003 f_angle_d 0.845 f_chiral_restr 0.034 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13500 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 349
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing