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Crystal structure of drug resistant V82S/V1082S HIV-1 Protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 Protein concentration - 2.2 mg/ml in Sodium Acetate buffer - 50mM Sodium Acetate and 0.1% Beta Mercaptoethanol pH 4.5
Precipitant - 0.9% Ammonium Sulphate in Phosphate Citrate buffer - 0.2M Sodium dihydrogen phosphate and 0.1M Trisodium Citrate pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.49 α = 90 b = 62.49 β = 90 c = 83.44 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 MAR scanner 345 mm plate 2012-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.44 33.04 89.2 6924 6182 1.5 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.57 50.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1LV1 2.45 31.25 3 1.5 5880 5260 274 89.46 0.1953 0.19216 0.1984 0.25597 0.2669 RANDOM 32.839
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 40.892 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 16.307 r_dihedral_angle_1_deg 7.016 r_angle_refined_deg 1.534 r_angle_other_deg 0.789 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_bond_other_d 0.005 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.892 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 16.307 r_dihedral_angle_1_deg 7.016 r_angle_refined_deg 1.534 r_angle_other_deg 0.789 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1508 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling