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Human MMP13 in complex with L-glutamate motif inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QJ2 3QJ2 catalytic domain only (Chain A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 PROTEIN-INHIBITOR SOLUTION: MMP13 AT 20 MG/ML CO-CRYSTALLIZED WITH E3P AT 1.1 MILLI-M. RESERVOIR SOLUTION: 17.5% PEG 20K, 0.1 M MES, 0.02 M NACL. CRYOPROTECTANT: 5% DIETHYLENE GLYCOL, 5% ETHYLENE GLYCOL, 5% MPD, 5% PROPYLENE GLYCOL, 5% DMSO, 5% GLYCEROL, 0.005 M 3-(-PYRIDINIO)-1-PROPANESULFONATE, 10% PEG 20K, 0.033 M SODIUM ACETATE, 0.033 M ADA, 0.033 M BICINE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.303 α = 90 b = 85.16 β = 90 c = 40.916 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 100 CCD ADSC QUANTUM 315r bent cylindrical mirror 2011-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972420 ESRF ID23-1
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 2.43 85.1 96.9 0.29 0.31 10.6 7.21 8412 8151 35.49
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 2.43 2.59 87.4 1.399 1.29 2.81 6.63 1231
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 3QJ2 catalytic domain only (Chain A) 2.43 40.916 1.34 8377 8127 369 97.02 0.1654 0.1622 0.2341 0.2069 RANDOM 24.782
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] -2.7543 1.2548 1.4995
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.949 f_angle_d 1.121 f_chiral_restr 0.083 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1347 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 58
Software Software Software Name Purpose DNA data collection PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling