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Crystal structure of human MMP-7 in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 20% w/v Polyethylene glycol 3350, 100mM Bis-Tris propane pH7.5, 200mM Sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.16 42.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.799 α = 90 b = 75.799 β = 90 c = 60.53 γ = 90
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 PILATUS3 6M 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00003 SLS X10SA
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 53.6 99.9 0.992 7.9 11.9 18920
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 1.79 0.54
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 53.598 18916 913 99.915 0.205 0.203 0.2177 0.2392 0.2504 18.838
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] -1.469 -1.469 2.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.937 r_dihedral_angle_4_deg 23.558 r_dihedral_angle_3_deg 13.236 r_dihedral_angle_1_deg 7.892 r_lrange_it 5.948 r_lrange_other 5.937 r_scangle_other 3.141 r_scangle_it 3.14 r_mcangle_it 2.47 r_mcangle_other 2.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.937 r_dihedral_angle_4_deg 23.558 r_dihedral_angle_3_deg 13.236 r_dihedral_angle_1_deg 7.892 r_lrange_it 5.948 r_lrange_other 5.937 r_scangle_other 3.141 r_scangle_it 3.14 r_mcangle_it 2.47 r_mcangle_other 2.468 r_scbond_other 1.888 r_scbond_it 1.886 r_angle_refined_deg 1.555 r_mcbond_it 1.52 r_mcbond_other 1.52 r_angle_other_deg 1.352 r_nbd_refined 0.207 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.167 r_nbd_other 0.157 r_symmetry_xyhbond_nbd_refined 0.155 r_metal_ion_refined 0.124 r_symmetry_nbd_refined 0.111 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1340 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing