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HIV-1 protease in complex with a carbamoyl decorated pyrrolidine-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQZ pdb entry 2PQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 2.25M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.77 α = 90 b = 84.8 β = 90 c = 46.06 γ = 90
Symmetry Space Group P 21 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 103 CCD MAR CCD 165 mm mirrors 2006-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.808 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 25 92.1 0.039 0.039 34.15 4.2 33531 33531 12.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 93.7 0.23 0.23 6.59 4.1 1687
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 (All) 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 FREE R pdb entry 2PQZ 1.5 10 2 4 33413 33413 1678 92.3 0.178 0.169 0.1683 0.1775 0.2017 0.1869 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 4 1590 1742.5
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.06 s_non_zero_chiral_vol 0.056 s_similar_adp_cmpnt 0.047 s_angle_d 0.031 s_from_restr_planes 0.0275 s_anti_bump_dis_restr 0.023 s_bond_d 0.01 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1507 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 54
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing