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Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol 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 2.85 56.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.604 α = 90 b = 94.927 β = 90 c = 120.406 γ = 90
Symmetry Space Group P 21 21 21
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 2004-03-26 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 20 100 0.09 13.8 5.2 53516 53516 -1.5 -3 14.7
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) 2 2.07 71.4 0.251 5.9 3.6 4064
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 19.94 50745 2727 92.96 0.20326 0.20189 0.216 0.22829 0.2419 RANDOM 25.406
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] -0.08 1.52 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.281 r_dihedral_angle_4_deg 21.727 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 6.37 r_scangle_it 2.474 r_scbond_it 1.569 r_angle_refined_deg 1.375 r_mcangle_it 1.057 r_angle_other_deg 0.913 r_mcbond_it 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.281 r_dihedral_angle_4_deg 21.727 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 6.37 r_scangle_it 2.474 r_scbond_it 1.569 r_angle_refined_deg 1.375 r_mcangle_it 1.057 r_angle_other_deg 0.913 r_mcbond_it 0.56 r_mcbond_other 0.114 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5172 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 261
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling