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Crystal structure of the outer domain of HIV-1 gp120 in complex with VRC-PG04 space group P3221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SE9 PDB ENTRY 3SE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 10% peg400, 20% peg8000, 100 mM Na-acetate pH5.5, 500 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.27 71.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.91 α = 90 b = 158.91 β = 90 c = 80.27 γ = 120
Symmetry Space Group P 32 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 CCD MARMOSAIC 300 mm CCD 2011-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 97.2 0.146 0.146 21.82 6 22975 2 75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 88.3 2.61 3
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 3SE9 3 43.65 1.34 22971 1380 97.2 0.186 0.183 0.1881 0.245 0.2493
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 17.339 f_angle_d 1.299 f_chiral_restr 0.083 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4806 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 53
Software Software Software Name Purpose XDS data scaling PHASER phasing PHENIX refinement XDS data reduction