3B8S

Crystal structure of wild-type chitinase A from Vibrio harveyi


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82881.20M Ammonium Sulfate, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.346.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.267α = 91.74
b = 64.283β = 91.18
c = 83.522γ = 112.91
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-01-18MSINGLE 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
1224.6294.60.0660.07619.54736937369319.517.7
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)
22.1191.90.2280.2635.5410404

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 3B9E224.627369369969372494.610.170220.170220.168360.2051RANDOM16.188
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]
0.37-0.710.3-0.97-0.210.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.885
r_dihedral_angle_3_deg12.437
r_dihedral_angle_4_deg10.338
r_dihedral_angle_1_deg5.165
r_scangle_it1.421
r_angle_refined_deg0.968
r_scbond_it0.946
r_mcangle_it0.597
r_mcbond_it0.453
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.885
r_dihedral_angle_3_deg12.437
r_dihedral_angle_4_deg10.338
r_dihedral_angle_1_deg5.165
r_scangle_it1.421
r_angle_refined_deg0.968
r_scbond_it0.946
r_mcangle_it0.597
r_mcbond_it0.453
r_nbtor_refined0.301
r_nbd_refined0.175
r_symmetry_hbond_refined0.153
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.112
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8708
Nucleic Acid Atoms
Solvent Atoms1091
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing