1UP3

Structure of the endoglucanase Cel6 from Mycobacterium tuberculosis in complex with METHYL-CELLOBIOSYL-4-DEOXY-4-THIO-BETA-D-CELLOBIOSIDE at 1.6 angstrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherCOMPLEX WITH SDP5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.514 % PEG 4K, 100 MM MES 6.5, 200 MM LISO4. THE PROTEIN WAS AT 10MG/ML AND INCUBATED WITH 1 MM OF LIGAND FOR 1 HOUR PRIOR CRYSTALLISATION. 30 % PEG 400 WAS ADDED AS CRYOPROTECTANT, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.0339.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.893α = 90
b = 93.058β = 90
c = 46.69γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCD2003-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.62098.60.09713.24.7356252
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)
11.61.6695.60.39333.7

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 REPLACEMENTTHROUGHOUTCOMPLEX WITH SDP51.619.8433839178598.20.140.1380.174RANDOM9.98
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]
0.08-0.20.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.49
r_scangle_it4.284
r_scbond_it2.628
r_angle_other_deg1.712
r_mcangle_it1.578
r_angle_refined_deg1.57
r_mcbond_it0.889
r_nbd_other0.256
r_symmetry_vdw_other0.247
r_nbd_refined0.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.49
r_scangle_it4.284
r_scbond_it2.628
r_angle_other_deg1.712
r_mcangle_it1.578
r_angle_refined_deg1.57
r_mcbond_it0.889
r_nbd_other0.256
r_symmetry_vdw_other0.247
r_nbd_refined0.219
r_symmetry_vdw_refined0.216
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.14
r_chiral_restr0.095
r_nbtor_other0.085
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
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_refined
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 Atoms2143
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling