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Human MMP12 (catalytic domain) in complex with AP316
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 25% PEG 6000, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.32 47.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.42 α = 90 b = 63.02 β = 90 c = 37.42 γ = 90
Symmetry Space Group P 21 21 2
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 OXFORD ONYX CCD 2015-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.540
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 2.2 46.7 99.9 0.26 10.9 11.6 8809 25.4
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 2.2 2.33 99.5 0.8 1.9 11.2
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 1RMZ 2.2 46.66 8357 439 99.78 0.1803 0.1778 0.1831 0.22712 0.2339 RANDOM 25.625
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] -1.04 0.68 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_4_deg 12.653 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 8.11 r_long_range_B_refined 6.806 r_long_range_B_other 6.748 r_scangle_other 3.432 r_angle_other_deg 2.491 r_mcangle_it 2.227 r_mcangle_other 2.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_4_deg 12.653 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 8.11 r_long_range_B_refined 6.806 r_long_range_B_other 6.748 r_scangle_other 3.432 r_angle_other_deg 2.491 r_mcangle_it 2.227 r_mcangle_other 2.127 r_angle_refined_deg 2.064 r_scbond_it 2.036 r_scbond_other 2.034 r_mcbond_it 1.395 r_mcbond_other 1.248 r_chiral_restr 0.084 r_bond_other_d 0.036 r_gen_planes_other 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 1246 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing