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Crystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 Protein: 6 microL hMMP9(E402A) at 181 micro-M 0.12 M acetohydroxamic acid and 0.3 microL IT34-I at 6.9 mill-M. Reservoir: 10% PEG 20K, 0.1 M MMT (L-malic acid, MES, Tris) 75% acid/25% basic, 0.8 M NaCl, 0.02 SrCl2, 0.01% azide. Cryoprotectant: CryoProtX CM2, 0.8 M Li formate, 0.1 M (MMT 75% acid/25% basic), 9% PEG 10K, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.2 α = 90 b = 57.4 β = 90 c = 172.03 γ = 90
Symmetry Space Group P 21 21 21
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 2012-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9184 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 1.698 50 99.7 0.174 0.168 9.91 8.97 38532 38427 -3 23.385
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 1.7 1.8 98.5 1.052 1.083 2.06 8.92 6144
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 (All) 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 4H3X 1.698 40.568 -3 2.01 38427 38419 1922 99.75 0.1602 0.1615 0.1597 0.1603 0.1954 0.1948 RANDOM 18.68
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 16.904 f_angle_d 1.084 f_chiral_restr 0.08 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2764 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 61
Software Software Software Name Purpose DNA data collection MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling