Experiment: 4PM3

Structure of the double-stranded DNA binding type IV secretion protein TraN from Enterococcus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4P0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	298	1:1 setup of purification buffer with Index screen condition 42 (0.1 M Bis-Tris, 25.0 % PEG 3350); final protein concentration: 3.25 mg/ml Crystal soaked for 1.5 h with Br4Pt

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.88	α = 90
b = 54.94	β = 91.89
c = 57.71	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	toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification)	2010-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0615	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	57.68	100	0.12	0.141	0.073	8.8	3.6	19191	19191			14.79

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		0.522	0.522	0.324	1.2	3.6	2804

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	FREE R-VALUE	4P0Z	1.8	28.967	1.34	19171	986	99.95	0.1716	0.1693	0.1732	0.2134	0.2144

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.216
f_angle_d	0.962
f_chiral_restr	0.042
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1886
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction