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HIV-1 Protease multiple mutant PRS5B with Darunavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 292 2.2 M Ammonium Phosphate and 100 mM Tris buffer at pH 7.9.
Crystal Properties Matthews coefficient Solvent content 3 59.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.001 α = 90 b = 74.001 β = 90 c = 93.983 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER X 16M 2018-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 1.66 50 98.5 0.066 0.076 0.037 0.999 18.1 4 31010 18.1
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 1.66 1.72 98.4 0.491 0.565 0.275 0.97 3.2 4.1
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 3NU3 1.66 37.03 29427 1537 98.55 0.18285 0.18115 0.1811 0.21471 0.2147 RANDOM 23.723
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.281 r_dihedral_angle_3_deg 12.844 r_dihedral_angle_4_deg 10.493 r_dihedral_angle_1_deg 6.983 r_long_range_B_refined 5.877 r_scbond_it 3.521 r_mcangle_it 3.205 r_mcbond_it 2.311 r_angle_refined_deg 1.861 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.281 r_dihedral_angle_3_deg 12.844 r_dihedral_angle_4_deg 10.493 r_dihedral_angle_1_deg 6.983 r_long_range_B_refined 5.877 r_scbond_it 3.521 r_mcangle_it 3.205 r_mcbond_it 2.311 r_angle_refined_deg 1.861 r_chiral_restr 0.136 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing