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Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 830C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100mM TrisHCl, 1500mM ammonium formate, 10.4% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.409 α = 90 b = 36.06 β = 131.09 c = 95.948 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 ADSC QUANTUM 315r 2012-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97645 ALS 5.0.3
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 1.2 50 94.9 0.051 15.5 3 104586
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 1.2 1.22 60.4 0.363 1.8
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 830C 1.2 33.75 104585 5238 94.9 0.1648 0.1638 0.1641 0.1854 0.1861 RANDOM 15.5145
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] 0.56 0.24 -0.19 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.51 r_dihedral_angle_4_deg 22.217 r_dihedral_angle_3_deg 11.104 r_dihedral_angle_1_deg 6.081 r_scangle_it 3.644 r_scbond_it 2.568 r_mcangle_it 1.921 r_angle_refined_deg 1.224 r_mcbond_it 1.08 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.51 r_dihedral_angle_4_deg 22.217 r_dihedral_angle_3_deg 11.104 r_dihedral_angle_1_deg 6.081 r_scangle_it 3.644 r_scbond_it 2.568 r_mcangle_it 1.921 r_angle_refined_deg 1.224 r_mcbond_it 1.08 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.202 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.118 r_metal_ion_refined 0.098 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2645 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 52
Software Software Software Name Purpose SCALEPACK data reduction REFMAC refinement PDB_EXTRACT data extraction SCALEPACK data scaling MOLREP phasing HKL data reduction