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Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 293 Protein: MMP9h Nter=GFQT E402Q V391Q at 384.3 micro-M with 120 milli-M AHA Reservoir: 10% MPEG 20K, 100mM PCTP 75/25, 1.5 NaCl. Cryoprotectant: 12.5% di-ethylene glycol, 12.5% DMSO, 12.5% MPD, 12.5% 1,2-propnaediol, 25% glycerol, 9% PEG 10K, 100 milli-M PCTP 80/20, 1.5 NaCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.9 α = 90.03 b = 98.86 β = 111.95 c = 47.13 γ = 89.98
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 2012-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 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 1.9 50 86.8 0.132 0.104 6.35 2.25 45622 -3 29.73
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 1.9 2.02 68.6 0.773 0.694 1.21 2.17
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 4H1Q 1.9 33.46 1.99 45622 45613 2512 87 0.209 0.207 0.241 0.293 19.98
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 18.183 f_angle_d 1.233 f_chiral_restr 0.081 f_plane_restr 0.015 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5100 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 223
Software Software Software Name Purpose DNA data collection MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling