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N74D 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 PEG 3350, NaI, Sodium Cacodylate, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.741 α = 90 b = 91.741 β = 90 c = 57.163 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 2015-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000030 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 2.9 45.87 99.8 0.123 0.129 0.039 0.999 16.7 11.2 6190
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 2.9 3.08 99.4 1.134 1.191 0.364 0.694 10.6
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 2.9 45.87 5866 323 99.87 0.2222 0.2194 0.2244 0.2736 0.2709 RANDOM 83.079
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] 1.4 0.7 1.4 -4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.603 r_sphericity_bonded 29.204 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 6.298 r_angle_refined_deg 1.904 r_angle_other_deg 1.072 r_chiral_restr 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.603 r_sphericity_bonded 29.204 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 6.298 r_angle_refined_deg 1.904 r_angle_other_deg 1.072 r_chiral_restr 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction