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Structure of the I124A 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, MIB, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.82 56.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.611 α = 90 b = 92.611 β = 90 c = 57.954 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 CMOS RDI CMOS_8M 2016-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000031 ALS 4.2.2
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 2.4 57.95 97.2 0.113 0.119 0.036 0.998 15.8 10.6 10933
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 2.4 2.49 96.8 0.75 0.797 0.267 0.808 8.4
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 2.4 57.95 10280 644 97.05 0.1925 0.1894 0.1957 0.2358 0.2378 RANDOM 48.192
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] 0.44 0.22 0.44 -1.44
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.627 r_dihedral_angle_2_deg 32.485 r_sphericity_bonded 30.535 r_dihedral_angle_4_deg 20.579 r_dihedral_angle_3_deg 12.505 r_dihedral_angle_1_deg 5.023 r_angle_refined_deg 1.06 r_angle_other_deg 0.881 r_chiral_restr 0.055 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.627 r_dihedral_angle_2_deg 32.485 r_sphericity_bonded 30.535 r_dihedral_angle_4_deg 20.579 r_dihedral_angle_3_deg 12.505 r_dihedral_angle_1_deg 5.023 r_angle_refined_deg 1.06 r_angle_other_deg 0.881 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1660 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 19
Software Software Software Name Purpose Aimless data scaling Blu-Ice data collection REFMAC refinement PDB_EXTRACT data extraction Aimless data reduction PHASER phasing