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Hexameric HIV-1 CA in complex with hexacarboxybenzene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5), Mellitic acid (1mM). Mellitic acid stock was adjusted to pH 8.0 with TRIS prior to setting up trays.
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.759 α = 90 b = 90.759 β = 90 c = 56.76 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 IMAGE PLATE RIGAKU RAXIS HTC 2015-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 45.38 97.9 0.105 0.043 0.997 11.7 6.8 19152
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.5 0.862 0.368 0.644 2.1 6.5 1357
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 3H4E 1.95 45.38 18188 964 97.8 0.195 0.1936 0.2015 0.2206 0.2272 RANDOM 31.245
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] 0.22 0.11 0.22 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.344 r_dihedral_angle_4_deg 21.454 r_dihedral_angle_3_deg 12.909 r_dihedral_angle_1_deg 5.465 r_mcangle_it 5.183 r_mcbond_it 3.991 r_mcbond_other 3.988 r_angle_refined_deg 1.281 r_angle_other_deg 0.899 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.344 r_dihedral_angle_4_deg 21.454 r_dihedral_angle_3_deg 12.909 r_dihedral_angle_1_deg 5.465 r_mcangle_it 5.183 r_mcbond_it 3.991 r_mcbond_other 3.988 r_angle_refined_deg 1.281 r_angle_other_deg 0.899 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1580 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 24
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction