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Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPG PDB ENTRY 1PPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 28%PEG4000,0.1MTRIS/HCL AT PH 8.2,0.7MLICL
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.712 α = 90 b = 72.712 β = 90 c = 69.583 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 IMAGE PLATE MARRESEARCH MAR IP M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.78 63.25 98.3 0.11 6.5 1 19759 1
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 1.78 1.87 89.5 0.88 0.9 1
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 PDB ENTRY 1PPG 1.78 63.25 18923 817 98.39 0.17146 0.17007 0.1759 0.20427 0.2074 RANDOM 30.91
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] 0.31 0.16 0.31 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.402 r_scangle_it 3.862 r_scbond_it 2.376 r_angle_refined_deg 1.52 r_mcangle_it 1.504 r_mcbond_it 0.864 r_symmetry_hbond_refined 0.315 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.402 r_scangle_it 3.862 r_scbond_it 2.376 r_angle_refined_deg 1.52 r_mcangle_it 1.504 r_mcbond_it 0.864 r_symmetry_hbond_refined 0.315 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1617 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling