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P38A/T216I mutant of the HIV-1 capsid protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 PEG3350, NaI, Sodium cacodylate, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.242 α = 90 b = 92.242 β = 90 c = 57.735 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 PIXEL DECTRIS PILATUS 6M 2016-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033190 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.6 46.8 99.8 0.071 0.075 0.024 0.998 15.8 9.8 8764
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.71 98.4 0.804 0.85 0.273 0.791 9.3
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 4XFX 2.6 46.8 8242 521 99.74 0.2029 0.2003 0.2093 0.241 0.2515 RANDOM 97.797
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] -0.65 -0.32 -0.65 2.11
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.941 r_sphericity_bonded 49.25 r_dihedral_angle_2_deg 34.549 r_dihedral_angle_4_deg 20.751 r_dihedral_angle_3_deg 13.73 r_dihedral_angle_1_deg 5.817 r_angle_refined_deg 1.266 r_angle_other_deg 0.925 r_chiral_restr 0.066 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.941 r_sphericity_bonded 49.25 r_dihedral_angle_2_deg 34.549 r_dihedral_angle_4_deg 20.751 r_dihedral_angle_3_deg 13.73 r_dihedral_angle_1_deg 5.817 r_angle_refined_deg 1.266 r_angle_other_deg 0.925 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1700 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 12
Software Software Software Name Purpose Aimless data scaling Blu-Ice data collection REFMAC refinement PDB_EXTRACT data extraction Aimless data reduction PHASER phasing