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Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2
reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2
drop ratio: 5ul protein + 1 ul reservoir, Vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.209 α = 90 b = 72.348 β = 90 c = 36.356 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MAR CCD 165 mm crystal monochromator 2001-09-28 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 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 2.04 50 100 0.067 0.067 13.4 2.6 19429 19429 -1.5 -3 20.9
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) 2.04 2.11 88 0.136 0.136 5.8 2.6 1948
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 FOURIER SYNTHESIS THROUGHOUT 2.05 50 18419 996 85.31 0.17033 0.16858 0.1748 0.20357 0.2119 RANDOM 19.235
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] 0.89 -0.21 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.937 r_dihedral_angle_4_deg 14.46 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 5.751 r_scangle_it 1.542 r_scbond_it 1.105 r_angle_refined_deg 1.067 r_angle_other_deg 0.796 r_mcangle_it 0.756 r_mcbond_it 0.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.937 r_dihedral_angle_4_deg 14.46 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 5.751 r_scangle_it 1.542 r_scbond_it 1.105 r_angle_refined_deg 1.067 r_angle_other_deg 0.796 r_mcangle_it 0.756 r_mcbond_it 0.462 r_symmetry_vdw_other 0.204 r_nbtor_refined 0.195 r_nbd_refined 0.192 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.139 r_symmetry_vdw_refined 0.139 r_symmetry_hbond_refined 0.139 r_metal_ion_refined 0.113 r_nbtor_other 0.082 r_mcbond_other 0.081 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2653 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing