3ARP

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


X-RAY DIFFRACTION

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
Matthew coefficientSolvent content
2.448.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.24α = 90
b = 50.97β = 99.53
c = 93.31γ = 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 X10SA0.97941SLSX10SA

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
11.5519.97696.70.04318.4685182-321.302
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)
11.551.59870.3220.3943

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 REPLACEMENTTHROUGHOUT3b9a1.5519.9768518042591000.14830.14630.187RANDOM16.8028
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]
0.160.420.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.387
r_dihedral_angle_4_deg15.171
r_dihedral_angle_3_deg12.491
r_dihedral_angle_1_deg6.449
r_scangle_it4.878
r_scbond_it3.336
r_angle_refined_deg2.391
r_mcangle_it2.337
r_mcbond_it1.468
r_chiral_restr0.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.387
r_dihedral_angle_4_deg15.171
r_dihedral_angle_3_deg12.491
r_dihedral_angle_1_deg6.449
r_scangle_it4.878
r_scbond_it3.336
r_angle_refined_deg2.391
r_mcangle_it2.337
r_mcbond_it1.468
r_chiral_restr0.172
r_bond_refined_d0.029
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4397
Nucleic Acid Atoms
Solvent Atoms884
Heterogen Atoms52

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction