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Crystal structure of chitinase 40 from thermophilic bacteria Streptomyces thermoviolaceus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other The model structure was generated by the GeneSilico Metaserver.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 1.9 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 4.01 69.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.15 α = 90 b = 183.15 β = 90 c = 130.814 γ = 120
Symmetry Space Group P 61 2 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 MARRESEARCH 2012-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.77 49 99.4 0.149 0.157 13.53 10.03 33170 33170 -3 57.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.77 2.94 98.1 1.008 1.063 1.91 9.79
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 The model structure was generated by the GeneSilico Metaserver. 2.771 49 1.36 33144 995 99.4 0.1515 0.1498 0.1569 0.2084 0.21 Random selection 64.2189
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 14.111 f_angle_d 1.478 f_chiral_restr 0.065 f_bond_d 0.014 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5572 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 14
Software Software Software Name Purpose XDS data reduction PHENIX model building PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing PHENIX refinement Aimless data scaling XSCALE data scaling XSCALE data reduction