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Structure of the T58A/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 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.646 α = 90 b = 91.646 β = 90 c = 57.695 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 2016-12-01 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 2.6 45.82 99.5 0.107 0.112 0.034 0.999 18.3 10.6 8617
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 96 1.391 1.469 0.466 0.577 9.7
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 45.8 8101 512 99.68 0.1931 0.1896 0.1959 0.2465 0.2481 RANDOM 69.192
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] -0.02 -0.01 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_sphericity_free 33.13 r_sphericity_bonded 32.167 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 13.513 r_dihedral_angle_1_deg 5.899 r_angle_refined_deg 1.315 r_angle_other_deg 0.931 r_chiral_restr 0.061 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_sphericity_free 33.13 r_sphericity_bonded 32.167 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 13.513 r_dihedral_angle_1_deg 5.899 r_angle_refined_deg 1.315 r_angle_other_deg 0.931 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1658 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 17
Software Software Software Name Purpose Aimless data scaling Blu-Ice data collection REFMAC refinement PDB_EXTRACT data extraction Aimless data reduction PHASER phasing