3ARZ

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with 2-(imidazolin-2-yl)-5-isothiocyanatobenzofuran


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B9A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop8.52931.1M Ammonium Sulfate, 0.1M Tris, pH 8.5, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.99α = 90
b = 85.21β = 112.87
c = 63.14γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9840SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8219.93697.50.06113.2551274-328.537
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)RedundancyNumber Unique Reflections (All)
11.821.8799.50.4550.553.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3b9a1.8219.93651274256497.650.14990.14770.1913RANDOM25.1078
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]
-0.49-0.53-0.750.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.824
r_dihedral_angle_3_deg13.797
r_dihedral_angle_4_deg13.025
r_dihedral_angle_1_deg5.945
r_angle_refined_deg2.109
r_chiral_restr0.177
r_bond_refined_d0.027
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4354
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms40

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction