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Crystal structure of MMP12 in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21212.
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 6.8 293 protein: hMMP12 689 micro-M + 10 milli-M hydroxamic acid in .2 M NaCl, .02 M TRIS pH 7.5, 3 milli-M CaCl2, 0.1 milli-M ZnCl2 + 1 milli-M RXP470.1-PEG-Cy5.5
precipitant: 20% PEG4K, 2% dioxane, 0.2 milli-M TRIS pH 9.5
cryoprotectant: 40% CM26 (12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 25 % 2,3-butanediol + 12.5 % DMSO), 25% MPEG 6K, 100 milii-M bistrisPhosphate/Na citrate pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.9 α = 90 b = 62.79 β = 90 c = 37.74 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 PIXEL DECTRIS PILATUS 6M mirrors 2015-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978570 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 2.07 50 99.9 0.15 0.139 10.15 4.69 19792 -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 2.07 2.13 100 1.278 1.67 4.73
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 4GQL 2.07 47.01 1.36 19713 986 99.6 0.208 0.206 0.2185 0.241 0.2487
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 17.061 f_angle_d 1.239 f_chiral_restr 0.035 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 152
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing