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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	291	0.1M Bis-Tris, pH 5.5, 25 % w/v PEG 3350, 2.5 mM NAD+

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.38

Crystal Data

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

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2018-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.21	47.03	89.1	0.998	5.8	1.8		467507			17.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.21	1.23	87.1		0.25		1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5dna	1.21	47.03	467501	23228	89.117	0.189	0.1882	0.2107	19.293

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]
-0.089	0.364	-0.141	0.014	-0.241	0.141

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.341
r_dihedral_angle_4_deg	13.945
r_dihedral_angle_3_deg	12.523
r_lrange_it	6.848
r_lrange_other	6.848
r_dihedral_angle_1_deg	6.704
r_scangle_it	5.826
r_scangle_other	5.826
r_scbond_it	4.501
r_scbond_other	4.501
r_mcangle_it	4.049
r_mcangle_other	4.049
r_mcbond_it	3.226
r_mcbond_other	3.226
r_angle_other_deg	2.296
r_angle_refined_deg	1.663
r_symmetry_nbd_refined	0.223
r_nbd_refined	0.214
r_symmetry_nbd_other	0.212
r_symmetry_xyhbond_nbd_refined	0.207
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.166
r_nbd_other	0.157
r_chiral_restr	0.095
r_ncsr_local_group_6	0.076
r_ncsr_local_group_1	0.073
r_ncsr_local_group_2	0.073
r_ncsr_local_group_5	0.072
r_symmetry_nbtor_other	0.069
r_ncsr_local_group_4	0.065
r_ncsr_local_group_3	0.062
r_symmetry_xyhbond_nbd_other	0.038
r_bond_other_d	0.034
r_gen_planes_other	0.02
r_bond_refined_d	0.012
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11621
Nucleic Acid Atoms
Solvent Atoms	1965
Heterogen Atoms	277

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MoRDa	phasing