5GZV

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
2.9558.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.989α = 90
b = 127.229β = 90
c = 161.406γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-12-03MSINGLE 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
12.650.0199.60.0641.447.470506
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)
12.62.6499.20.386.087.5

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 REPLACEMENTTHROUGHOUT1itx2.6150.0166976345999.030.205140.202630.25343RANDOM44.103
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]
0.180.02-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.417
r_dihedral_angle_3_deg18.364
r_dihedral_angle_4_deg17.355
r_dihedral_angle_1_deg7.917
r_long_range_B_refined7.735
r_long_range_B_other7.733
r_mcangle_it5.62
r_mcangle_other5.619
r_scangle_other5.093
r_mcbond_it3.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.417
r_dihedral_angle_3_deg18.364
r_dihedral_angle_4_deg17.355
r_dihedral_angle_1_deg7.917
r_long_range_B_refined7.735
r_long_range_B_other7.733
r_mcangle_it5.62
r_mcangle_other5.619
r_scangle_other5.093
r_mcbond_it3.586
r_mcbond_other3.586
r_scbond_it3.193
r_scbond_other3.191
r_angle_refined_deg1.812
r_angle_other_deg1.076
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms13479
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms68

Software

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