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Human MMP12 catalytic domain in complex with AP280
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% PEH 6000, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.43 α = 90 b = 62.58 β = 90 c = 37.5 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 2015-07-15 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 1.9 46.48 99.5 0.11 22.3 13.4 13391 28.3
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 1.9 2.01 98 0.8 2.6 11.1
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 1RMZ 1.9 46.48 12714 667 99.46 0.1688 0.16676 0.1761 0.20885 0.2136 RANDOM 27.782
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] -1.39 -0.16 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.873 r_dihedral_angle_4_deg 22.228 r_dihedral_angle_3_deg 12.182 r_dihedral_angle_1_deg 7.822 r_long_range_B_refined 7.472 r_long_range_B_other 7.369 r_scangle_other 3.9 r_angle_other_deg 2.513 r_scbond_it 2.422 r_scbond_other 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.873 r_dihedral_angle_4_deg 22.228 r_dihedral_angle_3_deg 12.182 r_dihedral_angle_1_deg 7.822 r_long_range_B_refined 7.472 r_long_range_B_other 7.369 r_scangle_other 3.9 r_angle_other_deg 2.513 r_scbond_it 2.422 r_scbond_other 2.42 r_mcangle_it 2.389 r_angle_refined_deg 2.336 r_mcangle_other 2.299 r_mcbond_it 1.582 r_mcbond_other 1.482 r_chiral_restr 0.093 r_bond_other_d 0.036 r_gen_planes_other 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 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 165 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing