3S6W

Crystal structure of Tudor domain of human TDRD3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	290	10% 2-propanol, 100mM Phosphate-Citrate, 0.2M Li2SO4, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.93	α = 90
b = 41.93	β = 90
c = 61.478	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	IMAGE PLATE	RIGAKU RAXIS IV++		2008-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.78	36.31	98.4				5836

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.84	100

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	1MHN	1.78	36.31	5573	263	98.38	0.18397	0.18291	0.20618	RANDOM	15.579

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]
0.27	0.13		0.27		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	41.335
r_dihedral_angle_2_deg	29.518
r_dihedral_angle_3_deg	13.534
r_dihedral_angle_1_deg	7.389
r_scangle_it	3.003
r_scbond_it	1.833
r_mcangle_it	1.364
r_angle_refined_deg	1.138
r_mcbond_it	0.733
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	428
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	8

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling