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Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 in complex with disaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 8.3% (w/v) PEG 3350, 1.3% (v/v) isopropanol, 33.3mM CaCl2, 33.3mM HEPES (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.041 α = 90 b = 99.041 β = 90 c = 242.143 γ = 120
Symmetry Space Group P 61 2 2
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 RAYONIX MX225HE 2011-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2 50 97.6 0.137 9.6 9.3 48576 47386
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 2 2.03 92.4 0.29 6.4 2182
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3W6B 2 34.62 48576 47114 2388 97.2 0.1824 0.1801 0.1813 0.2258 0.2271 RANDOM 33.1627
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.061 r_dihedral_angle_4_deg 16.356 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.069 r_scbond_it 2.942 r_angle_refined_deg 1.937 r_mcangle_it 1.715 r_mcbond_it 1.032 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.061 r_dihedral_angle_4_deg 16.356 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.069 r_scbond_it 2.942 r_angle_refined_deg 1.937 r_mcangle_it 1.715 r_mcbond_it 1.032 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4765 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 203
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling