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Crystal structure of the catalytic domain of chitinase ChiL from Chitiniphilus shinanonensis (CsChiL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ITX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M Tris-HCl, 0.2 M ammonium sulfate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.189 α = 90 b = 81.547 β = 90 c = 130.012 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 95 CCD ADSC QUANTUM 210r Focusing Mirror 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.25 50 97.3 0.061 0.066 0.027 25.3 5.9 197591 11.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 81.3 0.276 0.348 0.208 0.903 3.6 2.6
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-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 1ITX 1.25 27.69 186349 9893 96.66 0.1338 0.1324 0.1408 0.1606 0.1644 RANDOM 13.675
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] -0.91 1.53 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_3_deg 11.11 r_dihedral_angle_4_deg 8.98 r_dihedral_angle_1_deg 6.563 r_angle_other_deg 1.715 r_rigid_bond_restr 1.584 r_angle_refined_deg 1.345 r_chiral_restr 0.069 r_bond_other_d 0.015 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_3_deg 11.11 r_dihedral_angle_4_deg 8.98 r_dihedral_angle_1_deg 6.563 r_angle_other_deg 1.715 r_rigid_bond_restr 1.584 r_angle_refined_deg 1.345 r_chiral_restr 0.069 r_bond_other_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5834 Nucleic Acid Atoms Solvent Atoms 1520 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction