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Crystal structure of class I chitinase from Oryza sativa L. japonica
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 8%(w/v) PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.452 α = 90 b = 66.452 β = 90 c = 123.636 γ = 90
Symmetry Space Group P 43 21 2
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 4 2004-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2 33.22 99.8 0.05 0.05 10.1 13.7 19363 19363 25.237
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.05 99.8 0.238 0.238 3.2 13.8 1381
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2 33.22 19363 18386 976 100 0.17717 0.17717 0.17478 0.1806 0.22345 0.2237 RANDOM 25.254
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] 0.52 0.52 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.758 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 13.414 r_dihedral_angle_1_deg 6.016 r_scangle_it 3.15 r_scbond_it 2.188 r_angle_refined_deg 1.568 r_mcangle_it 1.508 r_mcbond_it 1.222 r_angle_other_deg 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.758 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 13.414 r_dihedral_angle_1_deg 6.016 r_scangle_it 3.15 r_scbond_it 2.188 r_angle_refined_deg 1.568 r_mcangle_it 1.508 r_mcbond_it 1.222 r_angle_other_deg 0.924 r_mcbond_other 0.257 r_nbd_refined 0.222 r_symmetry_vdw_other 0.211 r_nbd_other 0.194 r_nbtor_refined 0.189 r_symmetry_hbond_refined 0.175 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.098 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2148 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SOLVE phasing