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Structure of wild-type HIV protease in complex with degraded photosensitive inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDX
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 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.607 α = 90 b = 62.607 β = 90 c = 82.052 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 1.38 32.72 94.5 0.043 0.049 17.79 4.73 35441 -3 24.188
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 1.38 1.46 73.6 0.67 0.757 2.15
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 3NDX 1.38 35 35429 1772 94.56 0.2103 0.2083 0.2179 0.2474 0.2551 RANDOM 22.22
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] 0.11 0.05 0.11 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.652 r_dihedral_angle_4_deg 21.408 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 6.461 r_mcangle_it 3.094 r_angle_refined_deg 2.518 r_mcbond_it 2.32 r_mcbond_other 2.314 r_angle_other_deg 1.87 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.652 r_dihedral_angle_4_deg 21.408 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 6.461 r_mcangle_it 3.094 r_angle_refined_deg 2.518 r_mcbond_it 2.32 r_mcbond_other 2.314 r_angle_other_deg 1.87 r_chiral_restr 0.132 r_bond_refined_d 0.027 r_gen_planes_other 0.023 r_bond_other_d 0.014 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 80
Software Software Software Name Purpose XDS data reduction PDB_EXTRACT data extraction MOLREP phasing REFMAC refinement XSCALE data scaling