3DIN | pdb_00003din

Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TF2	PDB ENTRY 1TF2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	298	20% PEG 3350, 200mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.32	71.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.616	α = 90
b = 156.003	β = 90
c = 358.155	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315	Cryogenically cooled first crystal, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2007-08-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315	Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry	2007-10-17	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	ADSC QUANTUM 315	sagitally bent second mono crystal with 4:1 magnification ratio and vertically focusing mirror	2008-02-29	M	SINGLE WAVELENGTH
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97950	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97950	APS	24-ID-C
3	SYNCHROTRON	NSLS BEAMLINE X29A	0.97950	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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
1,2,3	4.5	50	97.7	0.065	16.1	11.6		34733

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3	4.5	4.77	89.7		0.85	2	8.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD, MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TF2	4.5	15	2	34733	34733	3269	97.7	0.279	0.279	0.29	0.303	0.29	RANDOM	358.2

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]
9.68			13.17		-22.85

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21
c_angle_deg	1.3
c_improper_angle_d	0.87
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21304
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	64

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
SOLVE	phasing
DM	phasing
CNS	refinement
PDB_EXTRACT	data extraction

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.