1UXX

CBM6ct from Clostridium thermocellum in complex with xylopentaose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GMMPDB ENTRY 1GMM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.620% PEG 1000, 0.2 M SODIUM ACETATE, 0.1 M ACETATE BUFFER PH4.6, pH 4.60
Crystal Properties
Matthews coefficientSolvent content
1.935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.48α = 90
b = 51.68β = 102.78
c = 36.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002003-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.65299.50.03163.413033
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)
11.61.6699.90.0949.13.4

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 1GMM1.651.991239164099.40.1820.180.222RANDOM13.52
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]
0.350.140.23-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.712
r_scangle_it3.355
r_scbond_it2.143
r_mcangle_it1.849
r_angle_refined_deg1.455
r_mcbond_it1.058
r_angle_other_deg0.83
r_symmetry_vdw_other0.314
r_symmetry_hbond_refined0.257
r_nbd_other0.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.712
r_scangle_it3.355
r_scbond_it2.143
r_mcangle_it1.849
r_angle_refined_deg1.455
r_mcbond_it1.058
r_angle_other_deg0.83
r_symmetry_vdw_other0.314
r_symmetry_hbond_refined0.257
r_nbd_other0.256
r_nbd_refined0.237
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.158
r_metal_ion_refined0.128
r_chiral_restr0.095
r_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
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_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 Atoms931
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing