2GSD

NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C2 in complex with NAD and azide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1M Bis-Tris, 1.8M Ammonium Sulfate, 5mM NAD, 5mM azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.45	α = 90
b = 66.5	β = 103.57
c = 75.55	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	293	IMAGE PLATE	MAR scanner 345 mm plate		2006-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ELLIOTT GX-6	1.5418

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	1.95	73.52	99.3	0.095			65949	28153			26.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.03	88

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLREP	THROUGHOUT	2NAD	1.95	73.52	65949	26730	1422	99.22	0.159	0.14441	0.14231	0.14	0.18385	0.18	RANDOM	18.954

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]
0.23		-0.57	0.14		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.619
r_dihedral_angle_4_deg	15.975
r_dihedral_angle_3_deg	14.032
r_dihedral_angle_1_deg	6.422
r_scangle_it	3.912
r_scbond_it	2.552
r_mcangle_it	1.659
r_angle_refined_deg	1.619
r_mcbond_it	1.06
r_nbtor_refined	0.301

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3084
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
XSCALE	data scaling
MOLREP	phasing

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.