5GZU

Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ITX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293(NH4)2HPO4, Na-citrate
Crystal Properties
Matthews coefficientSolvent content
2.9558.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.981α = 90
b = 127.99β = 90
c = 162.078γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9Photon FactoryBL-17A

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
12.0350.01990.05851.47.1149010
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.071000.3636.826.9

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 REPLACEMENTTHROUGHOUT1itx2.0350.01141163747698.820.184560.182350.22581RANDOM31.072
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]
-0.080.14-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.865
r_dihedral_angle_4_deg17.912
r_dihedral_angle_3_deg15.97
r_dihedral_angle_1_deg7.269
r_long_range_B_refined6.807
r_long_range_B_other6.751
r_scangle_other5.051
r_mcangle_it4.117
r_mcangle_other4.117
r_scbond_it3.407
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.865
r_dihedral_angle_4_deg17.912
r_dihedral_angle_3_deg15.97
r_dihedral_angle_1_deg7.269
r_long_range_B_refined6.807
r_long_range_B_other6.751
r_scangle_other5.051
r_mcangle_it4.117
r_mcangle_other4.117
r_scbond_it3.407
r_scbond_other3.406
r_mcbond_it2.967
r_mcbond_other2.966
r_angle_refined_deg2.011
r_angle_other_deg1.132
r_chiral_restr0.132
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13463
Nucleic Acid Atoms
Solvent Atoms1322
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing