7CLA

Crystal structure of HTH-type transcriptional regulator SkgA from Caulobacter crescentus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	289	13% ethanol, 100 mM NaCl, 5% MPD and 100 mM Tris-HCl pH 7.8

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.572	α = 90
b = 89.572	β = 90
c = 88.961	γ = 120

Symmetry
Space Group	P 65 2 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		2016-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97852	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	77.57	99.9	0.111	0.113	0.019	37.8	19.9		7759			36.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	99.5		1.145	0.299	0.748	1.75	13.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	3QAO	2.5	44.83	7010	383	95.6	0.2123	0.2092	0.2679	RANDOM	40.816

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]
-0.26	-0.13		-0.26		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.528
r_dihedral_angle_4_deg	26.181
r_dihedral_angle_3_deg	18.576
r_dihedral_angle_1_deg	5.576
r_angle_refined_deg	1.803
r_angle_other_deg	1.411
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.528
r_dihedral_angle_4_deg	26.181
r_dihedral_angle_3_deg	18.576
r_dihedral_angle_1_deg	5.576
r_angle_refined_deg	1.803
r_angle_other_deg	1.411
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1117
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
AutoSol	phasing
MOLREP	phasing
PHENIX	model building
Coot	model building

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 R01GM133198.