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Crystal Structure of the Wild-type Full-Length HIV-1 Capsid Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK4 PDB entries 1ak4, 1a43 experimental model PDB 1A43 PDB entries 1ak4, 1a43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 9-12% PEG 3350, 0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5, 0.01 M iron(III) chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.91 α = 90 b = 86.532 β = 99.73 c = 55.589 γ = 90
Symmetry Space Group P 1 21 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 315 2009-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.0 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 50 97.2 0.064 12.5 3.7 31847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 82.4 0.501 2.9 2706
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT R-free PDB entries 1ak4, 1a43 1.95 29.048 1.35 31042 1578 94.77 0.2064 0.2037 0.202 0.2534 0.251 random 36.4093
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] 3.9374 -8.4888 -5.9086 1.9712
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.649 f_angle_d 1.093 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3412 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 47
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction PHASER phasing