Experiment: 3JQO

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		EMD-5034

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	20-40% w/v MPD, 100mM Bis-Tris pH 6.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 202.4	α = 90
b = 211.63	β = 90
c = 203.44	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 315r	torroidal focussing mirrors	2009-02-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r	Adjustable focus mirrors	2009-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9755	ESRF	ID14-4
2	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.979	SOLEIL	PROXIMA 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	2.6	52.91	95.5	0.055	12.12	1.98	519405	496105	1	1	42

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	2.6	2.8	94.7		0.264	3.11	1.98	98005

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	EMDB entry 5034, Cryo-EM structure of trypsin digested core TraF/TraN/TraO complex	2.6	52.91	1	496104	12939	95.5	0.22885	0.22725	0.21	0.25935	0.23	RANDOM	37.277

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]
-2.54			5.12		-2.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.873
r_dihedral_angle_4_deg	20.24
r_dihedral_angle_3_deg	19.088
r_dihedral_angle_1_deg	8.146
r_scangle_it	4.962
r_scbond_it	3.123
r_angle_refined_deg	1.985
r_mcangle_it	1.678
r_mcbond_it	0.865
r_chiral_restr	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.873
r_dihedral_angle_4_deg	20.24
r_dihedral_angle_3_deg	19.088
r_dihedral_angle_1_deg	8.146
r_scangle_it	4.962
r_scbond_it	3.123
r_angle_refined_deg	1.985
r_mcangle_it	1.678
r_mcbond_it	0.865
r_chiral_restr	0.138
r_bond_refined_d	0.02
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37512
Nucleic Acid Atoms
Solvent Atoms	1290
Heterogen Atoms	40

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.