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Human MMP12 in complex with L-glutamate motif inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 MMP12 AT 0.4 mM co-crystallization, with 100mM AHA and non-chelating inhibitor EEG at 1.1 mM with reservoir: 27% PEG 10K, 0.1M glycine. AHA removed during cryo-soak for 5 min in 30% MPEG2K, 10% ethylene glycol, 200 mM imidazole malate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.09 α = 90 b = 63.65 β = 90 c = 37.37 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 2009-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.99190 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 1.59 33 99.6 0.099 0.081 16.2 7.67 23301 23208 25.7
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 1.59 1.68 98.8 0.632 0.805 2.89 7.58 3687
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LIK 1.587 32.976 2.01 23295 23181 1160 99.51 0.1797 0.1784 0.1752 0.203 0.2009 RANDOM
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] 0.3654 -0.1928 -0.1726
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.681 f_angle_d 1.612 f_chiral_restr 0.095 f_bond_d 0.016 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 56
Software Software Software Name Purpose DNA data collection MOLREP phasing PHENIX refinement XDS data reduction XSCALE data scaling