3GSD | pdb_00003gsd

2.05 Angstrom structure of a divalent-cation tolerance protein (CutA) from Yersinia pestis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NUH	PDB entry 2NUH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	Protein solution: 0.3M NaCl, 10mM HEPES pH 7.5. Well solution: 20% PEG 3350, 0.2M Sodium citrate, 0.1M HEPES pH 7.5. Cryo solution: 7% Glycerol, 7% Sucrose, 7% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.782	α = 90
b = 157.914	β = 90
c = 157.132	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 225 mm CCD	beryllium lenses	2009-02-27	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 Sym 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	2.05	29.59	98.1	0.094	17.7	5.9	107769	107769		-3	25.4

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	2.05	2.09	94.8		0.506	3.3	5	5167

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2NUH	2.05	29.59	101920	101920	5358	98.12	0.15868	0.15868	0.15648	0.15	0.20039	0.2	RANDOM	26.164

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]
-0.34			-0.64		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.891
r_dihedral_angle_4_deg	10.964
r_dihedral_angle_3_deg	9.493
r_scangle_it	5.079
r_scbond_it	3.361
r_dihedral_angle_1_deg	2.777
r_mcangle_it	2.002
r_angle_refined_deg	1.209
r_mcbond_it	1.191
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.891
r_dihedral_angle_4_deg	10.964
r_dihedral_angle_3_deg	9.493
r_scangle_it	5.079
r_scbond_it	3.361
r_dihedral_angle_1_deg	2.777
r_mcangle_it	2.002
r_angle_refined_deg	1.209
r_mcbond_it	1.191
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9936
Nucleic Acid Atoms
Solvent Atoms	1187
Heterogen Atoms	313

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.