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Crystal structure of MMP9 in complex with inhibitor BE4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein: human MMP9 E402Q 300 micro-M
Precipitant: 31.5% MPEG 5K; .14 M imidazole piperidine; pH 8.5
Cryoprotectant: 40% CM2 (25% di-ethylene glycol + 25% glycerol + 25% 1,2-propanediol), 10% PEG 10K, 200 milli-M NaCl, 100milli-M PCTP 50/50
Crystal Properties Matthews coefficient Solvent content 2.08 40.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.69 α = 90 b = 39.69 β = 90 c = 163.66 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER X 9M mirrors 2016-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.738001 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 1.1 54.55 98 0.147 0.155 0.998 9.35 10.4 1190339 114471 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.17 87.5 1.19 1.25 0.624 1.4 10.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5I12 1.104 31.69 1.26 114452 5704 98.88 0.1566 0.1557 0.1602 0.1722 0.1758 RANDOM
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 16.761 f_angle_d 0.802 f_chiral_restr 0.077 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1253 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing