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HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMZ PDB ENTRY 2NMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 Ammonium sulfate 40%, DMSO 10%, sodium citrate 0.25M. pH has been increased through ammonia diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.268 α = 90 b = 58.377 β = 90 c = 61.3 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm MIRRORS 2008-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.116 42.26 95.7 0.047 10.5 2.7 57890 69731 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.116 1.17 83.7 0.391 2.9 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2NMZ 1.116 42.26 2 66936 2796 96.77 0.17822 0.17683 0.1751 0.21139 0.2091 RANDOM 12.477
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] -0.52 0.08 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.552 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 12.496 r_dihedral_angle_1_deg 6.004 r_sphericity_free 5.956 r_scangle_it 4.46 r_sphericity_bonded 3.834 r_scbond_it 3.016 r_mcangle_it 2.181 r_mcbond_it 1.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.552 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 12.496 r_dihedral_angle_1_deg 6.004 r_sphericity_free 5.956 r_scangle_it 4.46 r_sphericity_bonded 3.834 r_scbond_it 3.016 r_mcangle_it 2.181 r_mcbond_it 1.588 r_rigid_bond_restr 1.587 r_angle_refined_deg 1.486 r_symmetry_hbond_refined 0.349 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 51
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling