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Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-hydroxy-2-(4-methoxy-N(2-(3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)ethyl)phenylsulfonamido)acetamide
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 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.394 α = 90 b = 60.446 β = 114.67 c = 54.043 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 2003-10-28 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 1.8 30.22 86.2 0.042 0.042 12.9 3.8 12054 12054 10.462
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) 1.8 1.9 24.7 0.115 0.115 6.4 1.3 490
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 1.81 30.22 10987 10987 1066 100 0.16585 0.16585 0.16079 0.1607 0.21899 0.2195 RANDOM 11.272
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] 0.03 -0.25 0.2 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.147 r_dihedral_angle_3_deg 10.971 r_sphericity_free 8.084 r_dihedral_angle_1_deg 5.924 r_dihedral_angle_4_deg 5.412 r_scangle_it 2.909 r_scbond_it 1.94 r_mcangle_it 1.234 r_angle_refined_deg 1.21 r_mcbond_it 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.147 r_dihedral_angle_3_deg 10.971 r_sphericity_free 8.084 r_dihedral_angle_1_deg 5.924 r_dihedral_angle_4_deg 5.412 r_scangle_it 2.909 r_scbond_it 1.94 r_mcangle_it 1.234 r_angle_refined_deg 1.21 r_mcbond_it 0.74 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.086 r_metal_ion_refined 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 146 Heterogen Atoms 36
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling