6VPW | pdb_00006vpw

1.90 Angstrom Resolution Crystal Structure Chemotaxis protein CheX from Vibrio vulnificus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H2D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	Protein: 10.4 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, Screen: Classics II (D7), 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.093	α = 90
b = 44.093	β = 90
c = 143.062	γ = 90

Symmetry
Space Group	P 41

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	C(111)	2019-07-24	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	1.9	30	99.9	0.056	0.056	0.063	0.028	25	5		21375		-3	33.2

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	1.9	1.93	100		0.791	0.791	0.887	0.397	0.823	2.3	4.8

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3h2d	1.9	28.58	20315	1027	99.87	0.1766	0.1741	0.2253	RANDOM	40.315

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]
1.06			1.06		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.339
r_dihedral_angle_4_deg	12.295
r_dihedral_angle_3_deg	11.575
r_dihedral_angle_1_deg	3.557
r_angle_refined_deg	1.333
r_angle_other_deg	0.322
r_chiral_restr	0.057
r_gen_planes_refined	0.056
r_gen_planes_other	0.053
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.339
r_dihedral_angle_4_deg	12.295
r_dihedral_angle_3_deg	11.575
r_dihedral_angle_1_deg	3.557
r_angle_refined_deg	1.333
r_angle_other_deg	0.322
r_chiral_restr	0.057
r_gen_planes_refined	0.056
r_gen_planes_other	0.053
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2264
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms

Software

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