3ARQ

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with IDARUBICIN


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop5.629316%(W/V) PEG 4000, 21%(v/v) propanol, 0.1M Na-Acetate, pH 5.6, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.01α = 90
b = 50.89β = 99.51
c = 93.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.87312SLSX10SA

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
11.519.92899.50.07223.4896142-318.599
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)
11.51.5498.90.4930.5336.9

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 REPLACEMENTTHROUGHOUT3b9a1.519.92896141480799.490.14650.14460.1836RANDOM14.9702
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]
-0.140.120.22-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.495
r_dihedral_angle_4_deg16.18
r_dihedral_angle_3_deg11.871
r_dihedral_angle_1_deg6.337
r_angle_refined_deg2.335
r_chiral_restr0.163
r_bond_refined_d0.029
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4405
Nucleic Acid Atoms
Solvent Atoms826
Heterogen Atoms54

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction