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Crystal structure of human proMMP-9 catalytic domain in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 25% w/v Polyethylene glycol 1500, 100mM SPG buffer pH5.0
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.04 α = 90 b = 73.82 β = 104.21 c = 77.68 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2022-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.99999 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.7 75.31 99.8 0.998 10.29 5.4 54815
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 0.617
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 49.17 52060 2754 99.87 0.18007 0.1782 0.188 0.21665 0.2229 RANDOM 36.249
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] -1.27 1.6 -0.42 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.508 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 13.007 r_long_range_B_refined 7.407 r_long_range_B_other 7.38 r_dihedral_angle_1_deg 7.137 r_scangle_other 5.648 r_mcangle_it 3.995 r_mcangle_other 3.99 r_scbond_it 3.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.508 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 13.007 r_long_range_B_refined 7.407 r_long_range_B_other 7.38 r_dihedral_angle_1_deg 7.137 r_scangle_other 5.648 r_mcangle_it 3.995 r_mcangle_other 3.99 r_scbond_it 3.873 r_scbond_other 3.86 r_mcbond_it 2.994 r_mcbond_other 2.992 r_angle_refined_deg 1.608 r_angle_other_deg 1.371 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3675 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing