4R2M

Crystal Structure of R134D mutant of YnaF (Universal Stress Protein F) from Salmonella typhimurium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Under oil, Microbatch	8.5	298	30% PEG 4000, 100mM Tris-HCl pH 8.5, 200mM Magnesium chloride, 5mM Adenosine 5'-(beta,gamma-imido)triphosphate, Under oil, Microbatch, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.18	α = 90
b = 131.18	β = 90
c = 33	γ = 90

Symmetry
Space Group	P 43 21 2

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	2014-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.978565	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	2.2	41.48	100	0.12		9.7		15273			32

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	2.2	2.32	100		0.676	3.5	9.9	2167

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 4R2L	2.2	41.48	14470	765	99.97	0.19728	0.19532	0.23435	RANDOM	41.254

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]
-0.29			-0.29		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.333
r_dihedral_angle_3_deg	13.272
r_dihedral_angle_4_deg	8.72
r_dihedral_angle_1_deg	6.245
r_long_range_B_refined	5.629
r_long_range_B_other	5.555
r_scangle_other	2.617
r_mcangle_it	2.276
r_mcangle_other	2.276
r_angle_refined_deg	1.814
r_scbond_it	1.701
r_scbond_other	1.701
r_mcbond_it	1.412
r_mcbond_other	1.411
r_angle_other_deg	0.806
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2074
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	64

Software

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