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Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant complex structure with Sanguinarine
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 5.5 293 26%(w/v) PEG 4000, 0.2M Ammonium Acetate, 0.1M Sodium Acetate, pH 5.5, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.69 α = 90 b = 83.34 β = 90 c = 102.76 γ = 90
Symmetry Space Group P 21 21 21
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 2009-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999989 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 2 19.956 99.8 0.085 18.72 39344 -3 27.361
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 2 2.05 100 0.407 0.435 6
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 2 19.956 39344 1968 100 0.148 0.1454 0.1472 0.1972 0.1993 RANDOM 21.5921
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] -0.26 0.48 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.394 r_dihedral_angle_4_deg 17.046 r_dihedral_angle_3_deg 14.495 r_dihedral_angle_1_deg 6.461 r_scangle_it 5.29 r_scbond_it 3.434 r_mcangle_it 2.12 r_angle_refined_deg 1.903 r_mcbond_it 1.215 r_chiral_restr 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.394 r_dihedral_angle_4_deg 17.046 r_dihedral_angle_3_deg 14.495 r_dihedral_angle_1_deg 6.461 r_scangle_it 5.29 r_scbond_it 3.434 r_mcangle_it 2.12 r_angle_refined_deg 1.903 r_mcbond_it 1.215 r_chiral_restr 0.173 r_bond_refined_d 0.024 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4359 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 56
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction