3N7U | pdb_00003n7u

NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein solution (2ml): 14 mg/ml FDH, 0.1M Na2HPO4, pH 7.0, 10 mM EDTA, 5mM sodium azide, 5mM NAD. Reservoir solution (2ml): 0.1M Bis-Tris, pH 5.5, 2.1M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 229.62	α = 90
b = 217.68	β = 92.62
c = 139.11	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MAR CCD 165 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.99	KURCHATOV SNC	K4.4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2	19.99	93.6	0.075	8.93	2.1	457766	428654			25.095

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	87.9		0.328	2.6	1.8	39349

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	19.99	434297	421051	22264	96.95	0.191	0.189	0.19	0.231	0.23	RANDOM	24.463

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]
0.61			-1.28		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.465
r_dihedral_angle_4_deg	17.014
r_dihedral_angle_3_deg	14.434
r_dihedral_angle_1_deg	6.457
r_scangle_it	3.742
r_scbond_it	2.415
r_angle_refined_deg	1.639
r_mcangle_it	1.419
r_mcbond_it	0.807
r_chiral_restr	0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.465
r_dihedral_angle_4_deg	17.014
r_dihedral_angle_3_deg	14.434
r_dihedral_angle_1_deg	6.457
r_scangle_it	3.742
r_scbond_it	2.415
r_angle_refined_deg	1.639
r_mcangle_it	1.419
r_mcbond_it	0.807
r_chiral_restr	0.113
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32868
Nucleic Acid Atoms
Solvent Atoms	3745
Heterogen Atoms	723

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.