3I2Z | pdb_00003i2z

Structure of cold shock protein E from Salmonella typhimurium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MJC	PDB code 1MJC; A decapeptide (residues 12-21) from the E. coli cold shock protein A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	290	28% PEG 20000, 0.05M AMPSO, 1% glycerol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.395	α = 90
b = 46.798	β = 103.84
c = 46.718	γ = 90

Symmetry
Space Group	P 1 21 1

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	Mirrors	2006-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.07400	SRS	PX10.1

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	1.1	45.36	99.82	0.047		5		47339	1.1	1.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.1	1.16	100		0.392	0.41	2.8	3.8	7261

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 1MJC; A decapeptide (residues 12-21) from the E. coli cold shock protein A	1.1	11.21	47339	2532	99.82	0.20506	0.20354	0.19	0.23424	0.23	RANDOM	18.862

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]
0.28		-0.92	1.8		-2.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.876
r_dihedral_angle_4_deg	26.446
r_dihedral_angle_3_deg	14.259
r_dihedral_angle_1_deg	7.058
r_angle_refined_deg	1.935
r_symmetry_hbond_refined	0.384
r_symmetry_vdw_refined	0.339
r_chiral_restr	0.312
r_nbtor_refined	0.304
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.131
r_bond_refined_d	0.02
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1073
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
SCALA	data scaling