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Crystal structure of MMP12 in complex with inhibitor BE4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 protein solution: hMMP12 at 314 micro-M + 10 milli-M acetohydroxamate + 1 milli-M BE4, 10% DMSO
precipitant: 38% PEG 4K, 0.16 M imidazole piperidine,15% Dioxane, pH 8.5.
Cryoprotectant: 40% CM15 (12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % MPD + 12.5 % glycerol + 12.5 % 1,2-propanediol + 12.5 % 1,4-dioxane + 12.5 mM NDSB 201), 25% PEG 6K, 100 milli-M TRIS HCl, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.19 α = 90 b = 63.32 β = 103.73 c = 78.32 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 9M microfocus 2016-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.976254 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) CC (Half) 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 1.48 43.44 99.4 0.127 0.137 0.997 7.85 6.67 100074 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.57 96.4 0.78 0.85 0.874 1.68 6.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5I4O 1.485 38.041 1.01 195903 9797 99.06 0.1732 0.1714 0.1728 0.2067 0.2076
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 21.579 f_angle_d 0.795 f_chiral_restr 0.079 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4932 Nucleic Acid Atoms Solvent Atoms 863 Heterogen Atoms 174
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building