6V9T

Tudor domain of TDRD3 in complex with a small molecule

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	1.2 M sodium citrate, 0.1 M Tris-HCl, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.855	α = 90
b = 83.855	β = 90
c = 114.045	γ = 120

Symmetry
Space Group	H 3 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	RAYONIX MX-300		2015-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.15	44.85	99.8	0.104	0.109	0.998	18.9	11.1		8558

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.22		98	0.982	1.03	0.884		11.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	pdb entry 3pmt	2.154	44.849	8557	699	99.837	0.198	0.1955	0.2289	42.789

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]
0.99	0.495		0.99		-3.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.964
r_dihedral_angle_3_deg	15.978
r_dihedral_angle_1_deg	8.607
r_lrange_other	7.143
r_lrange_it	7.142
r_scangle_it	5.385
r_scangle_other	5.381
r_mcangle_it	4.398
r_mcangle_other	4.394
r_scbond_it	3.888
r_scbond_other	3.885
r_mcbond_it	3.382
r_mcbond_other	3.379
r_angle_refined_deg	2.025
r_angle_other_deg	1.411
r_symmetry_xyhbond_nbd_refined	0.333
r_symmetry_nbd_refined	0.199
r_nbd_refined	0.187
r_nbtor_refined	0.186
r_nbd_other	0.184
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	868
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
PHASER	phasing
SCALEPACK	data scaling
Aimless	data scaling