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Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-hydroxy-2-(N-hydroxyethyl)biphenyl-4-ylsulfonamido)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 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.614 α = 90 b = 60.277 β = 115.2 c = 54.186 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 1.55 14.44 96.7 0.042 0.042 11.2 2 21123 21123 9.963
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) 1.55 1.63 82.3 0.212 0.212 3.5 1.2 2605
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 1.55 14.44 19177 19177 1945 100 0.13619 0.13619 0.13168 0.1318 0.1802 0.1797 RANDOM 13.663
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] 0.12 -0.06 -0.09 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.925 r_dihedral_angle_3_deg 10.952 r_dihedral_angle_4_deg 10.793 r_scangle_it 6.351 r_dihedral_angle_1_deg 6.125 r_scbond_it 4.889 r_mcangle_it 3.173 r_rigid_bond_restr 2.858 r_mcbond_it 2.341 r_angle_refined_deg 1.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.925 r_dihedral_angle_3_deg 10.952 r_dihedral_angle_4_deg 10.793 r_scangle_it 6.351 r_dihedral_angle_1_deg 6.125 r_scbond_it 4.889 r_mcangle_it 3.173 r_rigid_bond_restr 2.858 r_mcbond_it 2.341 r_angle_refined_deg 1.833 r_chiral_restr 0.145 r_bond_refined_d 0.025 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 29
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling