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Crystal structure of class I chitinase from Oryza sativa L. japonica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DKV PDB ENTRY 2DKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 11%(w/v) PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.082 α = 90 b = 117.082 β = 90 c = 77.971 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU JUPITER 210 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.57 101.53 97 0.06 0.06 10.5 9.5 17963 17963 39.187
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) 2.57 2.64 79.4 0.221 0.221 3.2 3.1 1143
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 2DKV 2.57 101.53 17963 967 100 0.18161 0.17858 0.1807 0.23609 0.2336 RANDOM 19.868
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] -0.36 -0.18 -0.36 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.264 r_dihedral_angle_4_deg 18.373 r_dihedral_angle_3_deg 15.287 r_dihedral_angle_1_deg 5.993 r_scangle_it 2.217 r_scbond_it 1.536 r_angle_refined_deg 1.398 r_mcangle_it 1.111 r_angle_other_deg 0.94 r_mcbond_it 0.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.264 r_dihedral_angle_4_deg 18.373 r_dihedral_angle_3_deg 15.287 r_dihedral_angle_1_deg 5.993 r_scangle_it 2.217 r_scbond_it 1.536 r_angle_refined_deg 1.398 r_mcangle_it 1.111 r_angle_other_deg 0.94 r_mcbond_it 0.892 r_chiral_restr 0.29 r_symmetry_vdw_other 0.231 r_nbd_refined 0.227 r_nbd_other 0.2 r_nbtor_refined 0.197 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.15 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_other 0.133 r_mcbond_other 0.128 r_nbtor_other 0.089 r_bond_refined_d 0.015 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 3729 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 40
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling