3ARX

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


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
2.449.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.11α = 90
b = 50.93β = 99.45
c = 93.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97935SLSX10SA

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
11.1640.65698.40.05912.52204668-315.495
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)
11.161.1988.10.2850.3633.3

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 REPLACEMENTTHROUGHOUT3b9a1.1640.6562046671023498.430.16190.16060.1852RANDOM17.4306
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]
0.030.070.35-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.519
r_dihedral_angle_4_deg19.96
r_dihedral_angle_3_deg11.79
r_dihedral_angle_1_deg6.507
r_angle_refined_deg2.597
r_chiral_restr0.155
r_bond_refined_d0.034
r_gen_planes_refined0.017
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4405
Nucleic Acid Atoms
Solvent Atoms1099
Heterogen Atoms50

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction