5GZT

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
1SMALL TUBES5.5297(NH4)2HPO4, Na-citrate
Crystal Properties
Matthews coefficientSolvent content
3.4364.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.339α = 90
b = 123.486β = 90
c = 130.856γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0SPring-8BL26B2

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
12.150.0199.90.04750.15.7108304
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)
12.12.141000.3674.425.5

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 REPLACEMENTTHROUGHOUT1itx2.150.01102679537099.730.177620.175350.2213RANDOM37.261
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]
-0.210.33-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.862
r_dihedral_angle_3_deg15.531
r_dihedral_angle_4_deg15.011
r_long_range_B_refined7.994
r_long_range_B_other7.834
r_dihedral_angle_1_deg7.488
r_scangle_other5.57
r_mcangle_it5.34
r_mcangle_other5.34
r_scbond_it3.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.862
r_dihedral_angle_3_deg15.531
r_dihedral_angle_4_deg15.011
r_long_range_B_refined7.994
r_long_range_B_other7.834
r_dihedral_angle_1_deg7.488
r_scangle_other5.57
r_mcangle_it5.34
r_mcangle_other5.34
r_scbond_it3.803
r_scbond_other3.761
r_mcbond_it3.746
r_mcbond_other3.746
r_angle_refined_deg1.985
r_angle_other_deg1.093
r_chiral_restr0.119
r_bond_refined_d0.021
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 Atoms9185
Nucleic Acid Atoms
Solvent Atoms1358
Heterogen Atoms36

Software

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