3MCR

Crystal structure of NADH dehydrogenase subunit C (Tfu_2693) from THERMOBIFIDA FUSCA YX-ER1 at 2.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	1.0000M 1,6-Hexanediol, 0.0100M CoCl2, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.264	α = 90
b = 69.264	β = 90
c = 114.21	γ = 90

Symmetry
Space Group	P 43 21 2

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.65	48.97	99.8	0.048	25.89	6.95		8611		-3	82.093

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)
1	2.65	2.74	100		0.81	2.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	2fug	2.65	48.97	8568	402	99.88	0.21	0.207	0.259	RANDOM	40.196

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]
1.75			1.75		-3.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.209
r_dihedral_angle_4_deg	11.895
r_dihedral_angle_3_deg	11.558
r_scangle_it	5.754
r_scbond_it	3.605
r_dihedral_angle_1_deg	2.987
r_mcangle_it	2.126
r_angle_refined_deg	1.41
r_mcbond_it	1.087
r_angle_other_deg	0.967

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.209
r_dihedral_angle_4_deg	11.895
r_dihedral_angle_3_deg	11.558
r_scangle_it	5.754
r_scbond_it	3.605
r_dihedral_angle_1_deg	2.987
r_mcangle_it	2.126
r_angle_refined_deg	1.41
r_mcbond_it	1.087
r_angle_other_deg	0.967
r_mcbond_other	0.174
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1222
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.