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HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9M PDB ENTRY 1G9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (5 MG/ML IN 0.35 M NACL, 0.005 M TRIS CL PH 7.0) + 0.35 UL OF RESERVOIR (50 UL OF NA ACETATE pH 4.5 + 250 UL OF HAMPTON CRYSTAL SCREEN REAGENT 18 + 126 UL OF ETHANOL + 292 UL OF WATER), pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.98 α = 90 b = 81.71 β = 90.37 c = 74.48 γ = 90
Symmetry Space Group C 1 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 100 CCD ADSC QUANTUM 4 2000-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9721 NSLS X4A
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 2.9 20 98.5 0.093 0.093 10.38 4.37 102604 23464 -3 60.5
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 2.9 3 97.1 0.439 0.439 2.33 3.3 2315
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1G9M 2.9 20 23385 23030 1160 96.8 0.2068 0.295 RANDOM 68.1
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] 5.426 8.516 -13.941
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.6 c_scangle_it 2.86 c_mcangle_it 2.82 c_scbond_it 1.738 c_mcbond_it 1.568 c_angle_deg 1.138 c_improper_angle_d 0.79 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7173 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 196
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement