3B9D

Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide


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
2.1843.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.508α = 90
b = 83.076β = 90
c = 105.586γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-02-01MSINGLE 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
11.7224.5499.20.0710.07726.36.8595615956117.2
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)
11.721.8195.60.1230.1369.95.68247

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 3B9E1.7224.545956156474302499.160.188410.188410.187030.2145RANDOM15.683
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]
-0.2-0.190.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.291
r_dihedral_angle_3_deg12.033
r_dihedral_angle_4_deg9.327
r_dihedral_angle_1_deg5.146
r_scangle_it1.337
r_angle_refined_deg0.962
r_scbond_it0.923
r_mcangle_it0.648
r_mcbond_it0.491
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.291
r_dihedral_angle_3_deg12.033
r_dihedral_angle_4_deg9.327
r_dihedral_angle_1_deg5.146
r_scangle_it1.337
r_angle_refined_deg0.962
r_scbond_it0.923
r_mcangle_it0.648
r_mcbond_it0.491
r_nbtor_refined0.302
r_nbd_refined0.17
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.129
r_xyhbond_nbd_refined0.087
r_chiral_restr0.07
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 Atoms664
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing