3AS0

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant complex structure with Sanguinarine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop5.529326%(w/v) PEG 4000, 0.2M Ammonium Acetate, 0.1M Sodium Acetate, pH 5.5, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.69α = 90
b = 83.34β = 90
c = 102.76γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.999989SLSX10SA

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
1219.95699.80.08518.7239344-327.361
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)
122.051000.4070.4356

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 REPLACEMENTTHROUGHOUT3b9a219.9563934419681000.1480.14540.1972RANDOM21.5921
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]
-0.260.48-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.394
r_dihedral_angle_4_deg17.046
r_dihedral_angle_3_deg14.495
r_dihedral_angle_1_deg6.461
r_scangle_it5.29
r_scbond_it3.434
r_mcangle_it2.12
r_angle_refined_deg1.903
r_mcbond_it1.215
r_chiral_restr0.173
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.394
r_dihedral_angle_4_deg17.046
r_dihedral_angle_3_deg14.495
r_dihedral_angle_1_deg6.461
r_scangle_it5.29
r_scbond_it3.434
r_mcangle_it2.12
r_angle_refined_deg1.903
r_mcbond_it1.215
r_chiral_restr0.173
r_bond_refined_d0.024
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4359
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms56

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction