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Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with 2-(imidazolin-2-yl)-5-isothiocyanatobenzofuran
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 5.6 293 16%(W/V) PEG 4000, 21%(v/v) propanol, 0.1M Na-Acetate, pH 5.6, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.08 α = 90 b = 51.03 β = 99.55 c = 93.27 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD 2009-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9840 SLS X10SA
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 1.35 19.972 97.3 0.053 16.19 129106 -3 18.103
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 95.9 0.505 0.589 2.8
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 3b9a 1.35 19.97 129105 6456 97.36 0.165 0.1635 0.1632 0.1942 0.1937 RANDOM 18.0873
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] -0.02 0.1 0.43 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.348 r_dihedral_angle_4_deg 17.017 r_dihedral_angle_3_deg 12.656 r_dihedral_angle_1_deg 6.538 r_angle_refined_deg 2.542 r_chiral_restr 0.168 r_bond_refined_d 0.032 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4405 Nucleic Acid Atoms Solvent Atoms 951 Heterogen Atoms 52
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction