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Structure of wild-type HIV protease in complex with photosensitive inhibitor PDI-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 291 200mM LiCl, 20% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.841 α = 90 b = 62.841 β = 90 c = 80.486 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 CCD MARMOSAIC 225 mm CCD 2012-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.61 10 99.7 0.04 0.045 20.76 5.1 23062 -3 32.025
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.71 99.8 0.635 0.711 2.57
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 3NDW 1.7 10 19632 978 98.88 0.2775 0.2749 0.2824 0.3262 0.2933 RANDOM 34.869
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.118 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_1_deg 7.225 r_mcangle_it 4.576 r_mcbond_it 3.244 r_mcbond_other 3.233 r_angle_refined_deg 2.191 r_angle_other_deg 1.401 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.118 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_4_deg 14.786 r_dihedral_angle_1_deg 7.225 r_mcangle_it 4.576 r_mcbond_it 3.244 r_mcbond_other 3.233 r_angle_refined_deg 2.191 r_angle_other_deg 1.401 r_chiral_restr 0.122 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1479 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 114
Software Software Software Name Purpose XDS data reduction PDB_EXTRACT data extraction MOLREP phasing REFMAC refinement XSCALE data scaling