3MST

Crystal structure of a Putative nitrate transport protein (TVN0104) from THERMOPLASMA VOLCANIUM at 1.35 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.33	277	0.25M calcium chloride, 14.0% 2-propanol, 0.1M sodium acetate pH 4.33, temperature 277K, NANODROP, VAPOR DIFFUSION, SITTING DROP
2	VAPOR DIFFUSION, SITTING DROP	4.33	277	0.25M calcium chloride, 22.0% 2-propanol, 0.1M sodium acetate pH 4.33, temperature 277K, NANODROP, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.042	α = 90
b = 80.04	β = 104.67
c = 42.522	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2010-03-10	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2010-02-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97959, 0.91837, 0.97917	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	1.35	41.13	99.5	0.055	14.71	4.88		49540		-3	19.818

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	1.35	1.4	96.5		0.503	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.35	41.13	49502	2500	99.59	0.121	0.119	0.155	RANDOM	18.029

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]
1.04		0.26	-0.48		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.163
r_dihedral_angle_4_deg	14.712
r_dihedral_angle_3_deg	12.329
r_scangle_it	6.852
r_dihedral_angle_1_deg	5.771
r_scbond_it	4.845
r_mcangle_it	3.535
r_mcbond_it	2.531
r_rigid_bond_restr	1.782
r_angle_refined_deg	1.661

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.163
r_dihedral_angle_4_deg	14.712
r_dihedral_angle_3_deg	12.329
r_scangle_it	6.852
r_dihedral_angle_1_deg	5.771
r_scbond_it	4.845
r_mcangle_it	3.535
r_mcbond_it	2.531
r_rigid_bond_restr	1.782
r_angle_refined_deg	1.661
r_angle_other_deg	0.984
r_mcbond_other	0.92
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1809
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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 R01GM133198.