1SZW

Crystal structure of E. coli tRNA pseudouridine synthase TruD

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG 5000MME, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.18	α = 90
b = 108.11	β = 90
c = 112.52	γ = 90

Symmetry
Space Group	P 21 21 21

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		2003-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.93219	BESSY	14.1

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	79.06	99.9	0.072	15.9		52753	52753	-3	-3

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	2.1	100		0.36

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	35	-3	51156	51075	1678	99.84	0.19397	0.19397	0.19246	0.23913	RANDOM	15.257

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]
0.06			-0.08		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.512
r_scangle_it	3.762
r_scbond_it	2.457
r_angle_refined_deg	1.659
r_mcangle_it	1.467
r_angle_other_deg	0.912
r_mcbond_it	0.898
r_symmetry_vdw_other	0.323
r_nbd_other	0.249
r_symmetry_hbond_refined	0.212
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.199
r_symmetry_vdw_refined	0.107
r_chiral_restr	0.106
r_nbtor_other	0.088
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5252
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
SHELXD	phasing