☰ Navigation Tabs
Crystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 8-16%(w/v) PEG8000, 1.0-1.5M ammonium formate, 0.1M Tris HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.372 α = 90 b = 36.058 β = 130.895 c = 95.298 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 IMAGE PLATE RIGAKU RAXIS V 2004-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0 SPring-8 BL32B2
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 1.98 29.65 98 0.085 9.3 3.69 24131
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 1.98 2.05 80.5 0.321 3.3 3.21 1975
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.98 29.65 24131 1220 97.99 0.177 0.1747 0.1747 0.2197 0.2164 RANDOM 27.5761
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] 0.84 -0.01 -0.14 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.29 r_dihedral_angle_4_deg 22.093 r_dihedral_angle_3_deg 14.657 r_dihedral_angle_1_deg 6.176 r_scangle_it 5.272 r_scbond_it 3.746 r_mcangle_it 2.575 r_mcbond_it 1.557 r_angle_refined_deg 1.318 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.29 r_dihedral_angle_4_deg 22.093 r_dihedral_angle_3_deg 14.657 r_dihedral_angle_1_deg 6.176 r_scangle_it 5.272 r_scbond_it 3.746 r_mcangle_it 2.575 r_mcbond_it 1.557 r_angle_refined_deg 1.318 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.131 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2656 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 88
Software Software Software Name Purpose d*TREK data reduction REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing