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Crystal Structure of a thermostable mutant of the Catalytic Domain of GH19 Chitinase from Gazyumaru, Ficus microcarpa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 18% (w/v) Polyethylene glycol 20K, 0.1 M sodium citrate (pH 5.0), and 3% (v/v) Glycerol.
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.579 α = 90 b = 38.894 β = 96.028 c = 177.739 γ = 90
Symmetry Space Group C 1 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 95 PIXEL DECTRIS PILATUS 2M-F 2017-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 47.58 96.6 0.998 12 3.4 799385
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 1.6 1.7 0.922
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4tx7 1.607 47.58 122333 6117 97.28 0.215 0.2137 0.2224 0.2437 0.2521 21.908
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] -0.016 0.008 0.008 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.518 r_dihedral_angle_3_deg 13.242 r_dihedral_angle_4_deg 12.623 r_dihedral_angle_1_deg 6.166 r_lrange_it 3.961 r_lrange_other 3.859 r_scangle_it 2.41 r_scangle_other 2.41 r_mcangle_other 2.136 r_mcangle_it 2.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.518 r_dihedral_angle_3_deg 13.242 r_dihedral_angle_4_deg 12.623 r_dihedral_angle_1_deg 6.166 r_lrange_it 3.961 r_lrange_other 3.859 r_scangle_it 2.41 r_scangle_other 2.41 r_mcangle_other 2.136 r_mcangle_it 2.135 r_scbond_it 1.514 r_scbond_other 1.511 r_angle_refined_deg 1.356 r_angle_other_deg 1.343 r_mcbond_it 1.342 r_mcbond_other 1.337 r_nbd_refined 0.206 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.166 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.141 r_symmetry_nbd_refined 0.101 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7541 Nucleic Acid Atoms Solvent Atoms 729 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data collection XDS data reduction PHASER phasing