5AFE

Medium Resolution structure of the C-terminal family 65 Carbohydrate Binding Module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens with a bound xyloglucan heptasaccharide (XXXG)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BA6PDB ENTRY 4BA6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30%(W/V) PEG 4000 CO-CRYSTALLISED WITH 10 MM OF HEPTASACCHARIDE XXXG CRYOPROTECTAN WAS 30% GLYCEROL ADDED TO ABOVE CRYSTALLISATION BUFFER
Crystal Properties
Matthews coefficientSolvent content
3.5865

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.96α = 90
b = 58.96β = 90
c = 117.1γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-07-25MSINGLE 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
12.658.9696.60.272.53.76535
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)
12.62.7497.21.50.63.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4BA62.652.66620630395.30.251220.248610.30613RANDOM71.468
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]
-0.12-0.120.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.556
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg6.178
r_mcangle_it1.768
r_scbond_it1.32
r_dihedral_angle_4_deg1.238
r_angle_refined_deg1.112
r_mcbond_other0.962
r_mcbond_it0.96
r_angle_other_deg0.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.556
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg6.178
r_mcangle_it1.768
r_scbond_it1.32
r_dihedral_angle_4_deg1.238
r_angle_refined_deg1.112
r_mcbond_other0.962
r_mcbond_it0.96
r_angle_other_deg0.645
r_chiral_restr0.068
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 Atoms977
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing