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Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-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 2.81 56.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.846 α = 90 b = 95.74 β = 90 c = 36.443 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 IMAGE PLATE RIGAKU RAXIS IV crystal monochromator 2005-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54
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 1.97 30 100 0.086 0.086 12.5 3.6 30135 30135 -0.5 -1 21.2
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) 1.97 2.04 96.2 0.39 0.39 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.97 26.14 28595 1502 97.54 0.17639 0.17422 0.2176 0.1892 RANDOM 25.065
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] -1.24 1.29 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.298 r_dihedral_angle_4_deg 24.012 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 5.709 r_scangle_it 1.575 r_angle_refined_deg 1.136 r_scbond_it 1.085 r_angle_other_deg 0.804 r_mcangle_it 0.718 r_mcbond_it 0.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.298 r_dihedral_angle_4_deg 24.012 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 5.709 r_scangle_it 1.575 r_angle_refined_deg 1.136 r_scbond_it 1.085 r_angle_other_deg 0.804 r_mcangle_it 0.718 r_mcbond_it 0.438 r_symmetry_vdw_other 0.212 r_nbtor_refined 0.195 r_nbd_refined 0.183 r_nbd_other 0.177 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.132 r_symmetry_vdw_refined 0.127 r_nbtor_other 0.083 r_mcbond_other 0.082 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2551 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 76
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling