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Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20D25N with Tucked Flap
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 298 0.9M sodium chloride and 0.2 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.08 40.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.148 α = 90 b = 48.569 β = 99.15 c = 69.68 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2011-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.8 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 45.9 93 0.049 27.3 3.8 59088
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 65.2 0.316 4.2 3.6
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 3UCB 1.45 9.92 55791 3070 92.81 0.14091 0.1382 0.1367 0.19077 0.1911 RANDOM 18.323
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] -0.04 -0.03 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.133 r_dihedral_angle_3_deg 12.26 r_scangle_it 8.528 r_dihedral_angle_1_deg 6.514 r_dihedral_angle_4_deg 6.208 r_scbond_it 5.769 r_mcangle_it 4.049 r_rigid_bond_restr 2.884 r_mcbond_it 2.739 r_angle_refined_deg 2.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.133 r_dihedral_angle_3_deg 12.26 r_scangle_it 8.528 r_dihedral_angle_1_deg 6.514 r_dihedral_angle_4_deg 6.208 r_scbond_it 5.769 r_mcangle_it 4.049 r_rigid_bond_restr 2.884 r_mcbond_it 2.739 r_angle_refined_deg 2.057 r_chiral_restr 0.157 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3036 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data scaling SERGUI data collection HKL-2000 data reduction PHASER phasing