☰ Navigation Tabs
Crystal structure of the catalytic domain of Human MMP12 in complex with a broad spectrum hydroxamate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein:(hMMP12 F171D at 927 micro-M + acetohydroxamic acid at 11.6 milli-M
Reservoir: 45% PEG 4,000
0.2 M imidazole piperidine
Cryoprotection: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10,000, 10% (AAB buffer 10% acid/90% basic) 0.2 M NaCl. Flash cooling in LN2.
, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.92 α = 90 b = 62.89 β = 90 c = 37.7 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 2011-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8726 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 1.5 50 99.7 0.114 0.107 14.21 7.98 27511 27420 -3 21.127
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 1.5 1.59 1.094 0.982 2.5 7.92 4379
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 3LJG 1.5 46.758 -3 2 27420 27413 1371 99.63 0.1662 0.165 0.1662 0.1884 0.1866 RANDOM 12.02
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 16.441 f_angle_d 1.079 f_chiral_restr 0.076 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 72
Software Software Software Name Purpose DNA data collection MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling