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Crystal structure of the catalytic domain of MMP-12 in complex with a twin inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein: hMMP12 F171D at 0.36 milli-M + 0.001 M AHA. Reservoir: 13% PEG 20,000
0.2 M imidazole malate
0.05 M NaCl Cryoprotectant: 27% PEG 8,000 15% MPEG 550, 10% glycerol, 0.09 M Tris-HCl , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.91 α = 90 b = 61.75 β = 90 c = 112.56 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 100 PIXEL DECTRIS PILATUS 6M mirrors 2012-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.8856 SOLEIL PROXIMA 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 1.43 50 99.7 0.059 0.053 19.29 5.82 61962 61752 -3 21.616
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 1.42 1.51 98.4 0.626 0.57 2.77 5.8 9880
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 4EFS 1.43 43.31 -3 1.99 61752 61749 3087 99.66 0.1577 0.1567 0.1576 0.1767 0.178 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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.272 f_angle_d 1.118 f_chiral_restr 0.078 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2492 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 127
Software Software Software Name Purpose DNA data collection MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling