6PTG

Structure of RNA polymerase binding protein and transcriptional regulator Dks from Chlamydia trachomatis L2 (LGV434)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Optimization screen HRCS_B5_PEG4000-3350, based on Hampton Research Crystal Screen B5, condition H3: 200mM Lithium sulfate, 25% (w/V) PEG 4000, 100mM Tris Base / HCl pH 8.5: ChtrB.19237.a.B1.PW38581 at 24mg/ml, grown at 14C: cryo: 15% EG: tray 310000 h3: puck lkp6-3

Crystal Properties
Matthews coefficient	Solvent content
3.32	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.42	α = 90
b = 83.42	β = 90
c = 99.03	γ = 120

Symmetry
Space Group	P 32 2 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	RAYONIX MX-300		2019-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.95	30.024	98.8	0.068	0.074	0.999	20.54	6.108		8668			63.378

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.03	98.9		0.625	0.682	0.89	3.12	6.225

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s	2.95	30.024	1.36	8651	835	98.99	0.1866	0.1823	0.2264	0	73.7569

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	13.278
f_angle_d	0.542
f_chiral_restr	0.039
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1270
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.