3B9A

Crystal structure of Vibrio harveyi chitinase A complexed with hexasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B9EPDB ENTRY 3B9E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP728816% (w/v) PEG 4000, 0.1M magnesium chloride, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.2244.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.704α = 90
b = 83.323β = 90
c = 106.565γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.83099.70.070.07426.38.5531315313126.315.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.847990.3120.3326.18.47564

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3B9E1.8305313150392267899.650.182230.182230.180760.21013RANDOM15.433
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]
0.150.07-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.225
r_dihedral_angle_3_deg11.961
r_dihedral_angle_4_deg9.499
r_dihedral_angle_1_deg5.103
r_scangle_it1.267
r_angle_refined_deg0.99
r_scbond_it0.844
r_mcangle_it0.637
r_mcbond_it0.375
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.225
r_dihedral_angle_3_deg11.961
r_dihedral_angle_4_deg9.499
r_dihedral_angle_1_deg5.103
r_scangle_it1.267
r_angle_refined_deg0.99
r_scbond_it0.844
r_mcangle_it0.637
r_mcbond_it0.375
r_nbtor_refined0.304
r_nbd_refined0.177
r_symmetry_vdw_refined0.144
r_xyhbond_nbd_refined0.099
r_chiral_restr0.069
r_symmetry_hbond_refined0.066
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4353
Nucleic Acid Atoms
Solvent Atoms690
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing