3ART

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


X-RAY DIFFRACTION

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
Matthew coefficientSolvent content
2.2645.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.6α = 90
b = 84.15β = 90
c = 102.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHhelios mirrors2009-01-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.2319.93698.30.08217.6428235-323.618
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)
12.232.2984.30.390.4474.6

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 REPLACEMENTTHROUGHOUT3b9a2.2319.9362823514121000.16490.16160.2287RANDOM16.7136
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]
-0.01-0.280.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.079
r_dihedral_angle_4_deg18.693
r_dihedral_angle_3_deg15.658
r_dihedral_angle_1_deg6.666
r_scangle_it4.333
r_scbond_it2.917
r_angle_refined_deg1.765
r_mcangle_it1.671
r_mcbond_it0.952
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.079
r_dihedral_angle_4_deg18.693
r_dihedral_angle_3_deg15.658
r_dihedral_angle_1_deg6.666
r_scangle_it4.333
r_scbond_it2.917
r_angle_refined_deg1.765
r_mcangle_it1.671
r_mcbond_it0.952
r_chiral_restr0.128
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4359
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms108

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction