3FKJ | pdb_00003fkj

Crystal structure of a putative phosphosugar isomerase (stm_0572) from salmonella typhimurium lt2 at 2.12 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	277	0.2000M NaThioCyanate, 20.0000% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.88	α = 90
b = 63.88	β = 90
c = 295.93	γ = 120

Symmetry
Space Group	P 65

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)	2008-11-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.90496,0.97858,0.97824	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	2.12	29.323	91.2	0.054	12.91	5.62		38085		-3	34.434

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	2.12	2.2	78.2		0.411	1.95

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	MAD	THROUGHOUT	2.12	29.323	38084	1899	98.88	0.167	0.165	0.17	0.212	0.21	RANDOM	36.186

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]
0.26	0.13		0.26		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.425
r_dihedral_angle_4_deg	17.767
r_dihedral_angle_3_deg	14.931
r_dihedral_angle_1_deg	6.286
r_scangle_it	5.647
r_scbond_it	4.16
r_mcangle_it	2.326
r_angle_refined_deg	1.413
r_mcbond_it	1.368
r_angle_other_deg	0.949
r_mcbond_other	0.373
r_nbd_refined	0.23
r_nbd_other	0.194
r_nbtor_refined	0.179
r_symmetry_vdw_other	0.163
r_xyhbond_nbd_refined	0.161
r_symmetry_vdw_refined	0.156
r_symmetry_hbond_refined	0.113
r_chiral_restr	0.089
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5188
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	6

Software

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