6R3M

Family 11 Carbohydrate-Binding Module from Clostridium thermocellum in complex with beta-1,3-1,4-mixed-linked tetrasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V0A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293.1520-28% (m/v) polyethyleneglycol (PEG) 3350, 0.2 M potassium phosphate, 0.1 M sodium acetate buffer pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.0540

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.249α = 90
b = 103.249β = 90
c = 39.58γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9763DiamondI02

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
11.4551.6299.80.07103.7277011
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)
11.451.4897.20.33.53.1

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 REPLACEMENTTHROUGHOUT1V0A1.4551.6226308139399.760.178540.176970.20798RANDOM13.81
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]
-0.1-0.05-0.10.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.968
r_dihedral_angle_3_deg12.313
r_dihedral_angle_4_deg10.817
r_dihedral_angle_1_deg7.521
r_long_range_B_refined4.339
r_scbond_it1.846
r_mcangle_it1.763
r_angle_refined_deg1.675
r_mcbond_it1.108
r_chiral_restr0.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.968
r_dihedral_angle_3_deg12.313
r_dihedral_angle_4_deg10.817
r_dihedral_angle_1_deg7.521
r_long_range_B_refined4.339
r_scbond_it1.846
r_mcangle_it1.763
r_angle_refined_deg1.675
r_mcbond_it1.108
r_chiral_restr0.287
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms1373
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing