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Crystal structure of a mutated catalytic domain of Human MMP12 in complex with RXP470
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 Protein : MMP12h F67D K241A 850 micro-M + 10mM AHA
Drop : 1 micro-L protein + 0.35 micro-l inhibitor(1.5 milli-M, DMSO)
Precipitant : 20% PEG4K, 0.2 M TRIS pH9.5
Cryo protectant : 5% diethylene glycol, 0% ethylene glycol, 5% MPD + 5% glycerol, 5% 2,3-butanediol, 5mM NDSB 201, 25% PEG 6K, 100mM TRIS HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.23 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.97 α = 90 b = 63.29 β = 90 c = 35.91 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 convex horizontal pre-focussing mirror (HPM) and a pair of focusing bimorph mirrors in Kirkpatrick-Baez (KB) 2015-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9184 SOLEIL PROXIMA 2
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 1.3 46.632 99.6 0.207 0.191 9.96 6.5 74325 74004 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.38 97.5 2.097 1.1 6.14
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4GQL 1.303 28.451 1.34 39081 1954 99.72 0.1468 0.1454 0.1489 0.1739 0.1749 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 14.101 f_angle_d 1.057 f_chiral_restr 0.07 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1242 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction MOLREP phasing Coot model building XDS data scaling