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Crystal Structure of the Catalytic Domain of a family GH18 Chitinase from fern, Peteris ryukyuensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SIM PDB ENTRY 3SIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 298 0.2M Magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.626 α = 90 b = 78.626 β = 90 c = 167.4 γ = 90
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 270 2012-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.57 71.17 99.7 0.068 68.92 7.4 70282
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 1.57 1.6 95.6 0.096 32.86 6.1 20606
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 PDB ENTRY 3SIM 1.57 50 66710 3550 99.67 0.15093 0.15019 0.1649 0.16488 0.1778 RANDOM 7.963
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] -0.51 -0.51 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_dihedral_angle_4_deg 18.697 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_1_deg 5.671 r_long_range_B_refined 2.295 r_long_range_B_other 2.019 r_angle_refined_deg 1.162 r_angle_other_deg 0.773 r_scangle_other 0.767 r_mcangle_it 0.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_dihedral_angle_4_deg 18.697 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_1_deg 5.671 r_long_range_B_refined 2.295 r_long_range_B_other 2.019 r_angle_refined_deg 1.162 r_angle_other_deg 0.773 r_scangle_other 0.767 r_mcangle_it 0.714 r_mcangle_other 0.714 r_scbond_it 0.464 r_scbond_other 0.464 r_mcbond_it 0.404 r_mcbond_other 0.403 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 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 4052 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling