5FU3

The complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AOTPDB ENTRY 5AOT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120 MM NA FORMATE 20MM NH4 ACETATE 20 MM NA3 CITRATE 20 MM NAK TARTRATE (RACEMIC) 20 MM NA OXAMATE 50 MM IMIDAZOLE 50 MM MES PH 6.5 12.5% MPD 12.5% PEG 1000 12.5% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0339

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.914α = 90
b = 54.753β = 94.67
c = 43.986γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002015-09-20MSINGLE 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
11.6143.8499.50.0417.53.6244391.5
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)
11.611.6499.60.671.63.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5AOT1.6143.8423157127099.410.198370.194940.25968RANDOM20.17
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]
1.01-1.76-0.950.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.684
r_sphericity_free30.705
r_sphericity_bonded18.447
r_dihedral_angle_3_deg13.469
r_dihedral_angle_1_deg7.956
r_dihedral_angle_4_deg5.079
r_rigid_bond_restr4.06
r_scbond_it3.709
r_mcangle_it3.143
r_mcbond_it2.553
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.684
r_sphericity_free30.705
r_sphericity_bonded18.447
r_dihedral_angle_3_deg13.469
r_dihedral_angle_1_deg7.956
r_dihedral_angle_4_deg5.079
r_rigid_bond_restr4.06
r_scbond_it3.709
r_mcangle_it3.143
r_mcbond_it2.553
r_mcbond_other2.519
r_angle_refined_deg1.823
r_angle_other_deg0.932
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms1509
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing