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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 2.84 56.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.883 α = 90 b = 96.457 β = 90 c = 36.638 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 ADSC QUANTUM 210 crystal monochromator 2005-06-12 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 2.2 30 100 0.112 0.112 14.5 4.8 22451 22451 -0.5 -1 27.3
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) 2.2 2.28 96.3 0.37 0.37 4.4 3.4 1895
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 2.3 29.8 18646 989 99.59 0.18602 0.1834 0.1881 0.23611 0.2359 RANDOM 8.15
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] -0.75 1.09 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 25.445 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 5.881 r_scangle_it 1.59 r_angle_refined_deg 1.153 r_scbond_it 1.092 r_angle_other_deg 0.804 r_mcangle_it 0.734 r_mcbond_it 0.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 25.445 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 5.881 r_scangle_it 1.59 r_angle_refined_deg 1.153 r_scbond_it 1.092 r_angle_other_deg 0.804 r_mcangle_it 0.734 r_mcbond_it 0.428 r_nbtor_refined 0.195 r_symmetry_vdw_other 0.193 r_symmetry_hbond_refined 0.189 r_nbd_refined 0.183 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.141 r_metal_ion_refined 0.11 r_nbtor_other 0.086 r_mcbond_other 0.08 r_chiral_restr 0.067 r_bond_refined_d 0.009 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 2531 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling