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Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZK pdb entry 1rzk
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 16% PEG 3350, 0.1M CaCl2, 0.1M Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.96 68.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 222.97 α = 90 b = 222.97 β = 90 c = 86.48 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 IMAGE PLATE MAR scanner 300 mm plate 2008-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 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 2.77 48.27 63.3 0.13 0.088 14.6 4.8 63180 39993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 12 0.456 0.61 1.2 1.9
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 1rzk 3.4 48.27 62593 31870 1520 93.64 0.2805 0.2796 0.2702 0.313 0.3006
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] -17.8341 -17.8341 -17.8485
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.585 f_angle_d 0.916 f_chiral_restr 0.04 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10548 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 350
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing