5ND6

Crystal structure of apo transketolase from Chlamydomonas reinhardtii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310 % w/v PEG 6K, 5 % v/v MPD and 0.1 M MES pH 6.5-7.0 or 0.1 M HEPES pH 7.0-8.0.
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.211α = 90
b = 74.311β = 119.3
c = 133.723γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.912ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.58116.698.10.0490.04912.73.31931023-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6497.90.5670.5671.9

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 REPLACEMENTTHROUGHOUT1ITZ1.58116.6180084951898.190.160970.159330.19225RANDOM26.221
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]
-0.46-0.743.18-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg19.488
r_dihedral_angle_3_deg14.549
r_long_range_B_refined8.549
r_long_range_B_other8.549
r_dihedral_angle_1_deg6.972
r_scangle_other5.14
r_mcangle_it4.429
r_mcangle_other4.429
r_scbond_it3.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg19.488
r_dihedral_angle_3_deg14.549
r_long_range_B_refined8.549
r_long_range_B_other8.549
r_dihedral_angle_1_deg6.972
r_scangle_other5.14
r_mcangle_it4.429
r_mcangle_other4.429
r_scbond_it3.374
r_scbond_other3.374
r_mcbond_it2.933
r_mcbond_other2.933
r_angle_refined_deg1.967
r_angle_other_deg1.154
r_chiral_restr0.144
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10233
Nucleic Acid Atoms
Solvent Atoms841
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing