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Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor (R)-2-(4-methoxyphenylsulfonamido)propanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y93 PDB ENTRY 1Y93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M TRIS, 30% PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.256 α = 90 b = 60.479 β = 116.17 c = 54.598 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 CCD OXFORD ONYX CCD Mirrors 2008-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 30.234 94.7 0.084 0.084 8.7 6.1 11191 11191 7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 81.4 0.224 0.224 6.3 2.8 1396
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1Y93 1.9 30.23 10199 10199 990 100 0.15935 0.15935 0.15505 0.1565 0.20418 0.2034 RANDOM 7.694
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] 0.18 0.04 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 14.065 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 6.417 r_sphericity_free 5.017 r_scangle_it 3.781 r_scbond_it 2.485 r_angle_refined_deg 1.626 r_mcangle_it 1.454 r_mcbond_it 0.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 14.065 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 6.417 r_sphericity_free 5.017 r_scangle_it 3.781 r_scbond_it 2.485 r_angle_refined_deg 1.626 r_mcangle_it 1.454 r_mcbond_it 0.855 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 22
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling