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Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470B
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 8.5 293 Protein complex: hMMP12 F171D 855 microM, inhibitor 0.788 milliM. Reservoir: 35% PEG 4,000
0.2M imidazole malate pH 8.5. Drops: 1 microL protein complex + 1 microL reservoir. Cryoprotectant: 40% MPEG 5K, 10% 1,2-propanediol, (10% (Na acetate, ADA, Bicine) 90% at pH 4/ 10% at pH 9.0). Flash freezing in Liquid N2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.77 α = 90 b = 62.76 β = 90 c = 37.84 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 4r mirrors 2010-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 95.6 0.111 0.0976 9.33 3.51 27502 26347 20.815
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 77.7 1.04 0.849 1.19 2.88 4388
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 4GQL 1.497 32.406 -3 1.99 26347 26336 1317 95.79 0.188 0.1864 0.1858 0.2178 0.2163 RANDOM 11.4
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 15.251 f_angle_d 1.107 f_chiral_restr 0.077 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 49
Software Software Software Name Purpose DNA data collection MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling