6FOP

Glycoside hydrolase family 81 from Clostridium thermocellum (CtLam81A), Mutant E515A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K3A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1530% (w/v) 2-methyl-2,4-pentanediol, 0.1M sodium acetate pH4,6 and 0.02M calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.6653.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.917α = 90
b = 139.033β = 90
c = 197.909γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9919ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.445.1599.50.0660.99814.76.6166379
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.42990.6080.9046.9

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 REPLACEMENTTHROUGHOUT4K3A1.445.15158020835699.370.10890.10770.1327RANDOM19.355
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]
1.36-0.48-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.419
r_sphericity_free31.595
r_dihedral_angle_4_deg11.692
r_dihedral_angle_3_deg10.593
r_sphericity_bonded10.287
r_dihedral_angle_1_deg6.316
r_rigid_bond_restr1.625
r_angle_refined_deg1.481
r_angle_other_deg0.959
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.419
r_sphericity_free31.595
r_dihedral_angle_4_deg11.692
r_dihedral_angle_3_deg10.593
r_sphericity_bonded10.287
r_dihedral_angle_1_deg6.316
r_rigid_bond_restr1.625
r_angle_refined_deg1.481
r_angle_other_deg0.959
r_chiral_restr0.095
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5660
Nucleic Acid Atoms
Solvent Atoms714
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing