1TO3 | pdb_00001to3

Structure of yiht from Salmonella typhimurium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 8% Glycerol; Cryoprotectant - 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 30% Glycerol, 1M NaBr, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.87	67.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.144	α = 90
b = 141.144	β = 90
c = 102.726	γ = 90

Symmetry
Space Group	I 41 2 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	MARRESEARCH	Vertical and horizontal focusing mirrors	2003-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979	APS	31-ID

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	2.7	20	99.2	0.123	9.4	5.4	14427	14427		-3	61

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)
	2.7	2.8	99.6		0.324	4.14

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	SAD	THROUGHOUT	2.7	20	-3	14392	14392	721	99.23	0.18018	0.18018	0.17867	0.18	0.20825	0.22	RANDOM	40.502

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]
-1.78			-1.78		3.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.692
r_dihedral_angle_3_deg	17.564
r_dihedral_angle_4_deg	16.662
r_dihedral_angle_1_deg	5.434
r_scangle_it	2.319
r_scbond_it	1.526
r_angle_refined_deg	1.467
r_mcangle_it	0.956
r_angle_other_deg	0.836
r_mcbond_it	0.831
r_symmetry_vdw_other	0.268
r_nbd_refined	0.222
r_nbd_other	0.195
r_symmetry_hbond_refined	0.191
r_xyhbond_nbd_refined	0.185
r_symmetry_vdw_refined	0.185
r_mcbond_other	0.119
r_nbtor_other	0.091
r_chiral_restr	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2218
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing