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Crystal structure of D157N mutant of Chitiniphilus shinanonensis chitinase ChiL (CsChiL) complexed with N,N'-diacetylchitobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.1 M Bis-Tris, 0.2 M NaCl, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.266 α = 90 b = 81.351 β = 90 c = 131.113 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 97 CCD ADSC QUANTUM 270 Focusing mirror 2015-12-19 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 Merge 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 1.95 50 97.8 0.102 0.112 0.046 8.8 5.7 54922
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 99 0.682 0.752 0.312 0.93 2.92 5.7
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 6KST 1.95 34.59 50006 2734 96.29 0.251 0.2485 0.2522 0.298 0.3012 RANDOM 31.626
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] -2.18 5.16 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_3_deg 14.994 r_dihedral_angle_4_deg 13.694 r_dihedral_angle_1_deg 7.611 r_angle_refined_deg 1.494 r_angle_other_deg 1.278 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_3_deg 14.994 r_dihedral_angle_4_deg 13.694 r_dihedral_angle_1_deg 7.611 r_angle_refined_deg 1.494 r_angle_other_deg 1.278 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5796 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction