3S93

Crystal structure of conserved motif in TDRD5

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			291	crystal used for final refinement: 1.5 M ammonium phosphate, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 8.5, vapor diffusion, temperature 291K
2			291	Selenomethionyl derivative: 1.5 M ammonium phosphat e, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 7, vapor diffusion, temperature 291K
3			291	crystal used for preliminary refinement: 25 w/v% PEG-3350, 0.2 M lithium sulfate, 0.1 M bis-tris propane. 1:200 trypsin was also added., pH 6.5, vapor diffusion, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.94	α = 90
b = 43.33	β = 90
c = 126.6	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	RIGAKU SATURN		2011-04-18	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC Q210 BINNED		2011-05-11	M	SINGLE WAVELENGTH
3	3	x-ray	100	CCD	MAR 300		2011-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E
2	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1
3	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-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	2.28	30	94.8	0.038	33.8			10833		-3	50.51

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	2.28	2.34	76.9		0.791	2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.28	27.48	10803	575		0.246	0.245	0.271	THIN SHELLS (SFTOOLS)	48.56

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]
2.5105			-3.3032		0.7928

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.08
t_omega_torsion	2.61
t_angle_deg	1.06
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1197
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XSCALE	data scaling
SOLVE	phasing
RESOLVE	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement