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Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with DEQUALINIUM
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 2.4 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.24 α = 90 b = 50.97 β = 99.53 c = 93.31 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 0.97941 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 1.55 19.976 96.7 0.043 18.46 85182 -3 21.302
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 1.55 1.59 87 0.322 0.394 3
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 1.55 19.976 85180 4259 100 0.1483 0.1463 0.1459 0.187 0.186 RANDOM 16.8028
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] 0.16 0.42 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.387 r_dihedral_angle_4_deg 15.171 r_dihedral_angle_3_deg 12.491 r_dihedral_angle_1_deg 6.449 r_scangle_it 4.878 r_scbond_it 3.336 r_angle_refined_deg 2.391 r_mcangle_it 2.337 r_mcbond_it 1.468 r_chiral_restr 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.387 r_dihedral_angle_4_deg 15.171 r_dihedral_angle_3_deg 12.491 r_dihedral_angle_1_deg 6.449 r_scangle_it 4.878 r_scbond_it 3.336 r_angle_refined_deg 2.391 r_mcangle_it 2.337 r_mcbond_it 1.468 r_chiral_restr 0.172 r_bond_refined_d 0.029 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4397 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 52
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction