6T8Z

NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A ternary complex with the oxidised form of the cofactor NAD+ and the substrate formate both at a primary and secondary sites.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DNA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.52910.1M Bis-Tris, pH 5.5, 25 % w/v PEG 3350, 2.5 mM NAD+
Crystal Properties
Matthews coefficientSolvent content
2.4349.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.395α = 85.689
b = 94.515β = 89.927
c = 94.33γ = 81.939
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.2147.0389.10.9985.81.846750717.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.211.2387.10.251.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5dna1.2147.034675012322889.1170.1890.18820.210719.293
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]
-0.0890.364-0.1410.014-0.2410.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.341
r_dihedral_angle_4_deg13.945
r_dihedral_angle_3_deg12.523
r_lrange_it6.848
r_lrange_other6.848
r_dihedral_angle_1_deg6.704
r_scangle_it5.826
r_scangle_other5.826
r_scbond_it4.501
r_scbond_other4.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.341
r_dihedral_angle_4_deg13.945
r_dihedral_angle_3_deg12.523
r_lrange_it6.848
r_lrange_other6.848
r_dihedral_angle_1_deg6.704
r_scangle_it5.826
r_scangle_other5.826
r_scbond_it4.501
r_scbond_other4.501
r_mcangle_it4.049
r_mcangle_other4.049
r_mcbond_it3.226
r_mcbond_other3.226
r_angle_other_deg2.296
r_angle_refined_deg1.663
r_symmetry_nbd_refined0.223
r_nbd_refined0.214
r_symmetry_nbd_other0.212
r_symmetry_xyhbond_nbd_refined0.207
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.166
r_nbd_other0.157
r_chiral_restr0.095
r_ncsr_local_group_60.076
r_ncsr_local_group_10.073
r_ncsr_local_group_20.073
r_ncsr_local_group_50.072
r_symmetry_nbtor_other0.069
r_ncsr_local_group_40.065
r_ncsr_local_group_30.062
r_symmetry_xyhbond_nbd_other0.038
r_bond_other_d0.034
r_gen_planes_other0.02
r_bond_refined_d0.012
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11621
Nucleic Acid Atoms
Solvent Atoms1965
Heterogen Atoms277

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MoRDaphasing