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Crystal structure of the peptidase domain of collagenase G from Clostridium histolyticum in complex with a hydroxamate-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Tris-Bicine pH 8.5,pentaethylene glycol, diethylene glycol, triethylene glycol,tetraethylene glycol, PEG 20,000 and PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.306 α = 90 b = 78.385 β = 90 c = 96.411 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 PILATUS3 6M 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 42.46 90.52 0.04 0.998 11.09 1.9 38367 23.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 91.91 0.773
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2y6i 1.8 42.46 38367 90.52 0.1796 0.1799 0.2073 0.2073 34.04
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 5.4627 f_angle_d 1.1054 f_chiral_restr 0.0668 f_bond_d 0.0139 f_plane_restr 0.0105
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3110 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing