4R2J | pdb_00004r2j

Crystal structure of YdaA (Universal Stress Protein E) from Salmonella typhimurium

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Under oil, Microbatch	5.8	298	0.2M Magnesium Nitrate hexahydrate, 20% PEG 3350, 10mM Adenosine 5'-(beta,gamma-imido)triphosphate, 0.2% n-dodecyl beta-D-maltoside, pH 5.8, Under oil, Microbatch, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.77	α = 90
b = 85.77	β = 90
c = 74.991	γ = 120

Symmetry
Space Group	P 31 2 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	bent collimating mirror and toroid	2011-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97625	ESRF	BM14

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	2.36	42.88	99.8	0.119		5.7		13536			45.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.48	98.9		0.642	2.2	5.5	1929

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 ID 3OLQ	2.36	37.14	12849	667	99.79	0.21435	0.21193	0.21	0.26186	0.26	RANDOM	59.55

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]
1.15	0.57		1.15		-3.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.784
r_dihedral_angle_4_deg	18.201
r_dihedral_angle_3_deg	17.712
r_long_range_B_refined	7.263
r_dihedral_angle_1_deg	6.673
r_mcangle_it	3.951
r_scbond_it	3.876
r_mcbond_it	2.678
r_angle_refined_deg	1.734
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.784
r_dihedral_angle_4_deg	18.201
r_dihedral_angle_3_deg	17.712
r_long_range_B_refined	7.263
r_dihedral_angle_1_deg	6.673
r_mcangle_it	3.951
r_scbond_it	3.876
r_mcbond_it	2.678
r_angle_refined_deg	1.734
r_chiral_restr	0.102
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2115
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	34

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.