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HIV-1 Protease - Epoxydic Inhibitor Complex (pH 6 - 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 6 298 Ammonium sulfate 40%, DMSO 10%, sodium citrate 0.25M, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.294 α = 90 b = 58.392 β = 90 c = 61.026 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 1.2 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 1.45 13.56 96.1 0.073 10.4 3.5 31849 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 1.45 1.5 76.4 0.0456 1.9 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2NMZ 1.45 13.56 2 32844 30233 1617 96.2 0.2034 0.18722 0.18412 0.1782 0.24574 0.2391 RANDOM 14.163
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] -0.05 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 21.715 r_dihedral_angle_3_deg 13.79 r_sphericity_free 8.489 r_scangle_it 6.056 r_dihedral_angle_1_deg 5.976 r_sphericity_bonded 4.592 r_scbond_it 4.325 r_mcangle_it 3.022 r_rigid_bond_restr 2.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 21.715 r_dihedral_angle_3_deg 13.79 r_sphericity_free 8.489 r_scangle_it 6.056 r_dihedral_angle_1_deg 5.976 r_sphericity_bonded 4.592 r_scbond_it 4.325 r_mcangle_it 3.022 r_rigid_bond_restr 2.501 r_mcbond_it 2.388 r_angle_refined_deg 1.967 r_symmetry_hbond_refined 0.352 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.214 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.13 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 177 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling