7KPO | pdb_00007kpo

High Resolution Crystal Structure of the DNA-binding Domain from the Sensor Histidine Kinase ChiS from Vibrio cholerae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	Protein: 6.3 mg/ml, 0.01M Tris pH 8.3; Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.912	α = 90
b = 78.606	β = 90
c = 72.372	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 300 mm CCD	Be	2019-12-11	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)	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	1.28	30	99.7	0.076	0.076	0.083	0.032	28.3	6.9		38590		-3	14.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.28	1.3	97.3		0.757	0.757	0.854	0.386	0.637	2.3	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	THROUGHOUT	1.28	25.97	36482	1885	99.68	0.146	0.1443	0.14	0.1803	0.18	RANDOM	18.571

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]
0.12			-0.06		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.72
r_dihedral_angle_4_deg	10.412
r_dihedral_angle_3_deg	8.541
r_dihedral_angle_1_deg	2.805
r_rigid_bond_restr	1.645
r_angle_refined_deg	1.217
r_angle_other_deg	0.362
r_chiral_restr	0.055
r_gen_planes_refined	0.052
r_gen_planes_other	0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.72
r_dihedral_angle_4_deg	10.412
r_dihedral_angle_3_deg	8.541
r_dihedral_angle_1_deg	2.805
r_rigid_bond_restr	1.645
r_angle_refined_deg	1.217
r_angle_other_deg	0.362
r_chiral_restr	0.055
r_gen_planes_refined	0.052
r_gen_planes_other	0.047
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	882
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

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.