☰ Navigation Tabs
MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OW9 PDB Entry 2OW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Dissolved in DMSO inhibitor was mixed with protein (protein concentration: 1mg/ml) at 5:1 ratio, 0.1 M acetohydrohamic acid added. Ternary complex was concentrated (to 17 mg/ml protien concentration). 1-2 uL hagind drops were mixed with same amount of reservoit solution (2.1 M ammonium sulfate in 0.1 M Hepes buffer) , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.836 α = 90 b = 71.974 β = 124.59 c = 138.13 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 210 mirrors 2001-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 90.7 0.096 6.5 2.3 160245 69624 26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 62.8 0.342 2 4793
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 (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 2OW9 2.3 50 56296 53427 2869 96.4 0.253 0.248 0.2464 0.34 0.3371 RANDOM 23.737
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 17.244 r_dihedral_angle_3_deg 16.114 r_dihedral_angle_1_deg 6.291 r_scangle_it 1.367 r_angle_refined_deg 1.172 r_scbond_it 0.889 r_mcangle_it 0.885 r_mcbond_it 0.506 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 17.244 r_dihedral_angle_3_deg 16.114 r_dihedral_angle_1_deg 6.291 r_scangle_it 1.367 r_angle_refined_deg 1.172 r_scbond_it 0.889 r_mcangle_it 0.885 r_mcbond_it 0.506 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.217 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.173 r_metal_ion_refined 0.125 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10558 Nucleic Acid Atoms Solvent Atoms 1024 Heterogen Atoms 316
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction MOLREP phasing