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Envelope glycoprotein gp120 core from HIV type 2 bound to the first two domains of human soluble CD4 receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NXY 2NXY,3LQA experimental model PDB 3LQA 2NXY,3LQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.15M DL-Malic acid 7.0, 0.1M imidazole pH 7.0, 22% PEGMME 550
Crystal Properties Matthews coefficient Solvent content 3.92 68.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.276 α = 90 b = 100.223 β = 90 c = 199.139 γ = 90
Symmetry Space Group C 2 2 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 2014-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0332 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 3 99.57 99.2 0.081 0.042 12.8 4.5 19116
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 2NXY,3LQA 3 99.57 17394 1721 99.12 0.23545 0.23053 0.2385 0.28673 0.285 RANDOM 103.142
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] 0.51 4.81 -5.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.426 r_dihedral_angle_3_deg 16.135 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_1_deg 7.987 r_long_range_B_refined 6.781 r_long_range_B_other 6.781 r_scangle_other 2.392 r_mcangle_it 2.302 r_mcangle_other 2.302 r_angle_refined_deg 1.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.426 r_dihedral_angle_3_deg 16.135 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_1_deg 7.987 r_long_range_B_refined 6.781 r_long_range_B_other 6.781 r_scangle_other 2.392 r_mcangle_it 2.302 r_mcangle_other 2.302 r_angle_refined_deg 1.486 r_scbond_it 1.391 r_scbond_other 1.391 r_mcbond_it 1.263 r_mcbond_other 1.262 r_angle_other_deg 1.058 r_chiral_restr 0.18 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3708 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction