3IIC | pdb_00003iic

Crystal structure of CheC-like superfamily protein (YP_001095400.1) from Shewanella SP. PV-4 at 2.13 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.2	277	0.2000M K2HPO4, 20.0000% PEG-3350, No Buffer pH 9.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.646	α = 90
b = 52.075	β = 90
c = 134.429	γ = 90

Symmetry
Space Group	P 21 21 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 325 mm CCD	Flat mirror (vertical focusing)	2009-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.13	48.564	99.2	0.073	10.88	3.94		17765		-3	36.717

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	2.13	2.21	99.2		0.564	2.4

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	2.13	48.564	17733	907	99.37	0.213	0.211	0.22	0.256	0.27	RANDOM	40.646

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]
4.54			-2.24		-2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.258
r_dihedral_angle_3_deg	12.084
r_dihedral_angle_1_deg	4.026
r_scangle_it	2.528
r_angle_refined_deg	1.722
r_scbond_it	1.718
r_angle_other_deg	1.301
r_mcangle_it	0.943
r_mcbond_it	0.513
r_mcbond_other	0.141

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.258
r_dihedral_angle_3_deg	12.084
r_dihedral_angle_1_deg	4.026
r_scangle_it	2.528
r_angle_refined_deg	1.722
r_scbond_it	1.718
r_angle_other_deg	1.301
r_mcangle_it	0.943
r_mcbond_it	0.513
r_mcbond_other	0.141
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2298
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	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.