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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 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.388 α = 90 b = 73.176 β = 103.66 c = 76.163 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 PILATUS 200K 2019-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54056
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 1.9 22 99 0.992 7.8 3.7 37682
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 1.9 2 0.829
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 1.9 22.01 35778 1899 98.85 0.17471 0.17301 0.1836 0.20643 0.2171 RANDOM 17.304
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] -0.17 0.65 0.76 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.148 r_dihedral_angle_4_deg 22.448 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 7.203 r_long_range_B_refined 5.244 r_long_range_B_other 5.201 r_scangle_other 3.288 r_mcangle_it 2.393 r_mcangle_other 2.39 r_scbond_it 2.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.148 r_dihedral_angle_4_deg 22.448 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 7.203 r_long_range_B_refined 5.244 r_long_range_B_other 5.201 r_scangle_other 3.288 r_mcangle_it 2.393 r_mcangle_other 2.39 r_scbond_it 2.109 r_scbond_other 2.077 r_angle_refined_deg 1.71 r_angle_other_deg 1.534 r_mcbond_it 1.476 r_mcbond_other 1.472 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 3667 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing