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Crystal Structure of HIV-1 Protease (Q7K) in Complex with Lopinavir
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.5 M NaCl, 100 mM citrate buffer pH 5.4-5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.707 α = 90 b = 85.417 β = 90 c = 46.233 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 100 CCD ADSC QUANTUM 4 2004-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 1.008 NSLS X4A
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 1.54 25.7 99.27 0.093 0.093 13.6 5.2 35654
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 1.537 1.577 91.54 0.702 0.702 3.04 3.9 2380
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.54 25.7 35654 3609 99.27 0.184 0.181 0.215 RANDOM 13.473
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] -0.07 0.05 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.069 r_dihedral_angle_3_deg 11.261 r_dihedral_angle_4_deg 9.969 r_dihedral_angle_1_deg 6.058 r_scangle_it 3.182 r_scbond_it 2.029 r_angle_refined_deg 1.5 r_mcangle_it 1.251 r_mcbond_it 0.842 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.069 r_dihedral_angle_3_deg 11.261 r_dihedral_angle_4_deg 9.969 r_dihedral_angle_1_deg 6.058 r_scangle_it 3.182 r_scbond_it 2.029 r_angle_refined_deg 1.5 r_mcangle_it 1.251 r_mcbond_it 0.842 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1516 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling