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Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RHH PDB ENTRY 1RHH AND 1RZK experimental model PDB 1RZK PDB ENTRY 1RHH AND 1RZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.50
Crystal Properties Matthews coefficient Solvent content 3.28 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.993 α = 90 b = 225.993 β = 90 c = 97.968 γ = 120
Symmetry Space Group P 6 2 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 MARRESEARCH 2004-03-12 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 3.3 20 86.6 0.082 0.082 26.2 9.6 19372 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.42 20.9 0.505 1.3 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1RHH AND 1RZK 3.3 20 22571 19364 1920 86.2 0.319 0.319 0.2849 0.349 0.3156 RANDOM 126.2
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] 11.12 19.38 11.12 -22.25
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_angle_deg 0.98 c_improper_angle_d 0.64 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_angle_deg 0.98 c_improper_angle_d 0.64 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7396 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 121
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling CNS refinement HKL-2000 data reduction CNS phasing