3ARV

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


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
2.3948.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.23α = 90
b = 50.82β = 99.49
c = 93.39γ = 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
11.539.87398.90.06316.6295965-318.398
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)
11.51.5494.70.1530.1848.1

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 REPLACEMENTTHROUGHOUT3b9a1.539.879596447991000.1460.14440.1774RANDOM15.2226
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]
0.140.090.11-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.822
r_dihedral_angle_4_deg16.63
r_dihedral_angle_3_deg12.105
r_dihedral_angle_1_deg6.543
r_scangle_it5.142
r_scbond_it3.393
r_mcangle_it2.504
r_angle_refined_deg2.437
r_mcbond_it1.494
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.822
r_dihedral_angle_4_deg16.63
r_dihedral_angle_3_deg12.105
r_dihedral_angle_1_deg6.543
r_scangle_it5.142
r_scbond_it3.393
r_mcangle_it2.504
r_angle_refined_deg2.437
r_mcbond_it1.494
r_chiral_restr0.161
r_bond_refined_d0.029
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4405
Nucleic Acid Atoms
Solvent Atoms847
Heterogen Atoms68

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction