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Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ED7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.7 M Sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 4.22 70.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.48 α = 90 b = 120.48 β = 90 c = 106.41 γ = 90
Symmetry Space Group P 43 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 315r 2011-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.17 53.88 96.9 0.072 14.7 4.9 40464 32.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.23 98.4 0.579 2.3 5
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 FREE R-VALUE 1ED7 2.17 48.67 1.34 40433 2026 96.3 0.1692 0.168 0.1747 0.1907 0.1963 Random selection
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 15.181 f_angle_d 0.872 f_chiral_restr 0.032 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2761 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction xia2 data scaling PHASER phasing GDA data collection