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Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor paramethoxy-sulfonyl-glycine hydroxamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 0.1 M Tris-HCl, 30% PEG 6000, 200 mM AHA, 1.0 M LiCl2 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.708 α = 90 b = 60.251 β = 115.16 c = 54.144 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 2005-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA
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 25.81 90.6 0.034 0.034 27.2 2.9 12682 12682 9.95
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 48.2 0.057 0.057 13.8 1.7 966
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 1Y93 1.8 25.81 11546 11546 1134 100 0.17081 0.17081 0.16805 0.1676 0.19965 0.1985 RANDOM 9.595
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] -0.01 -0.13 0.12 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.842 r_dihedral_angle_3_deg 12.451 r_dihedral_angle_4_deg 10.714 r_dihedral_angle_1_deg 6 r_scangle_it 3.021 r_scbond_it 2.06 r_mcangle_it 1.232 r_angle_refined_deg 1.202 r_mcbond_it 0.803 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.842 r_dihedral_angle_3_deg 12.451 r_dihedral_angle_4_deg 10.714 r_dihedral_angle_1_deg 6 r_scangle_it 3.021 r_scbond_it 2.06 r_mcangle_it 1.232 r_angle_refined_deg 1.202 r_mcbond_it 0.803 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.131 r_metal_ion_refined 0.119 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 22
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling