4V2X

High resolution structure of the full length tri-modular endo-beta-1, 4-glucanase B (Cel5B) from Bacillus halodurans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NDZPDB ENTRY 3NDZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M CALCIUM ACETATE, 0.1 M CACODYLATE PH 6.5, 8% PEG 8K WITH 30% GLYCEROL ADDED TO ABOVE AS CRYOPROTECTANT
Crystal Properties
Matthews coefficientSolvent content
2.2245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.22α = 90
b = 141.84β = 90
c = 50.82γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.6451.2799.90.0719.77.266600
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)
11.641.6899.80.742.66.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3NDZ1.6451.2763160337699.890.155620.15430.18094RANDOM19.389
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]
-0.70.220.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.041
r_dihedral_angle_4_deg16.311
r_dihedral_angle_3_deg11.23
r_dihedral_angle_1_deg5.804
r_scbond_it1.93
r_mcangle_it1.846
r_mcbond_it1.135
r_mcbond_other1.119
r_angle_refined_deg1.066
r_angle_other_deg0.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.041
r_dihedral_angle_4_deg16.311
r_dihedral_angle_3_deg11.23
r_dihedral_angle_1_deg5.804
r_scbond_it1.93
r_mcangle_it1.846
r_mcbond_it1.135
r_mcbond_other1.119
r_angle_refined_deg1.066
r_angle_other_deg0.704
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4334
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
BALBESphasing