6T92

NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex of N120C mutant protein with the reduced form of the cofactor NADH and the substrate formate at a secondary site.

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	7.5	291	0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 10 % w/v PEG 1000, 10 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.731	α = 85.627
b = 94.606	β = 89.88
c = 94.614	γ = 81.618

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	1.12	63.93	82.1	0.998	5.7	1.7		548213			15.7

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	1.12	1.14	53.2		0.291	0.8	1.4

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	1.12	63.93	548212	27331	82.101	0.208	0.2069	0.2276	18.109

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]
-0.172	-0.052	-0.041	0.793	0.069	-0.651

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.156
r_dihedral_angle_4_deg	14.201
r_dihedral_angle_3_deg	13.08
r_dihedral_angle_1_deg	6.819
r_lrange_other	6.113
r_lrange_it	6.112
r_scangle_it	5.084
r_scangle_other	5.083
r_scbond_it	3.963
r_scbond_other	3.963
r_mcangle_it	3.785
r_mcangle_other	3.785
r_mcbond_it	3.013
r_mcbond_other	3.013
r_angle_other_deg	2.339
r_angle_refined_deg	1.92
r_symmetry_nbd_refined	0.253
r_nbd_other	0.248
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_refined	0.216
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.163
r_xyhbond_nbd_other	0.135
r_chiral_restr	0.103
r_ncsr_local_group_5	0.074
r_ncsr_local_group_6	0.072
r_symmetry_nbtor_other	0.071
r_ncsr_local_group_4	0.069
r_ncsr_local_group_1	0.066
r_ncsr_local_group_2	0.066
r_ncsr_local_group_3	0.063
r_bond_other_d	0.034
r_gen_planes_other	0.032
r_gen_planes_refined	0.018
r_bond_refined_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11503
Nucleic Acid Atoms
Solvent Atoms	1759
Heterogen Atoms	256

Software

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