4AV6 | pdb_00004av6

Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase at 4 A in complex with phosphate and magnesium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		HIGH RESOLUTION RESTING STATE TMPPASE STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				35% PEG 400, 50 MM TRIS PH 8.0, 50 MM LISO4, 50 MM NASO4

Crystal Properties
Matthews coefficient	Solvent content
3.24	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.8	α = 90
b = 112.266	β = 103
c = 109.714	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 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	4	30	98.2	0.09	8.85	4.3		17075		-3	178.27

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	4	4.22	96.8		0.97	1.82	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	HIGH RESOLUTION RESTING STATE TMPPASE STRUCTURE	4	29.832	2.01	17061	863	98.88	0.2988	0.2952	0.29	0.365	0.36	239

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]
35.461		-23.7725	-24.6168		-10.8441

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.051
f_angle_d	2.169
f_chiral_restr	0.111
f_plane_restr	0.011
f_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9376
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	30

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	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.