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Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B5O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100mM TrisHCl, 1000mM ammonium formate, 15.3% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.798 α = 90 b = 36.281 β = 130.14 c = 96.382 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 2012-08-03 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 1.6 50 97.1 0.074 13.8 3.8 46398
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 1.6 1.63 68.5 0.443 2.8
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 5B5O 1.6 36.84 46396 2346 96.96 0.175 0.1733 0.1781 0.208 0.2128 RANDOM 24.4984
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] 0.93 -1.16 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.218 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_1_deg 5.549 r_scangle_it 4.609 r_scbond_it 3.247 r_mcangle_it 2.183 r_mcbond_it 1.423 r_angle_refined_deg 1.181 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.218 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_1_deg 5.549 r_scangle_it 4.609 r_scbond_it 3.247 r_mcangle_it 2.183 r_mcbond_it 1.423 r_angle_refined_deg 1.181 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.202 r_nbd_refined 0.187 r_metal_ion_refined 0.182 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2648 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 70
Software Software Software Name Purpose SCALEPACK data reduction PDB_EXTRACT data extraction SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL data reduction