5AOT

Very high resolution structure of a novel carbohydrate binding module from Ruminococcus flavefaciens FD-1 endoglucanase Cel5A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AOSPDB ENTRY 5AOS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.520 MG/ML OF PROTEIN IN 0.2 M SODIUM ACETATE, 0.1 M CACODYLIC ACID PH 6.5, 30%(W/V) POLYETHYLENE GLYCOL 8000. 30%(V/V) GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT.
Crystal Properties
Matthews coefficientSolvent content
1.8534

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.272α = 90
b = 45.02β = 90
c = 49.453γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
11.0233.2999.60.0516.26.242277
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)
11.021.0596.50.941.55.4

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 5AOS1.0233.2947545247299.640.164720.164430.17028RANDOM14.359
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]
1.16-0.43-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.36
r_sphericity_free23.507
r_dihedral_angle_3_deg11.738
r_sphericity_bonded11.287
r_dihedral_angle_4_deg10.626
r_dihedral_angle_1_deg7.476
r_rigid_bond_restr2.923
r_scbond_it2.044
r_mcangle_it1.66
r_angle_refined_deg1.613
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.36
r_sphericity_free23.507
r_dihedral_angle_3_deg11.738
r_sphericity_bonded11.287
r_dihedral_angle_4_deg10.626
r_dihedral_angle_1_deg7.476
r_rigid_bond_restr2.923
r_scbond_it2.044
r_mcangle_it1.66
r_angle_refined_deg1.613
r_mcbond_it1.277
r_mcbond_other1.234
r_angle_other_deg0.757
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms802
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing