5M9N

Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B9X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	30% PEG4000, 0.2M MgCl2, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.91	α = 64.94
b = 52.962	β = 88.85
c = 59.619	γ = 67.67

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.0282	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	29.34	96.9	0.034	0.025	16.7	3.5		30788			33.712

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	1.95	1.99	89.8		0.411	2.3	3.5

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	4B9X	1.95	29.34	29186	1600	96.91	0.21482	0.21222	0.26035	RANDOM	44.441

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]
-0.57	1.66	0.06	-3.11	0.17	3.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.716
r_dihedral_angle_3_deg	14.718
r_dihedral_angle_4_deg	12.824
r_dihedral_angle_1_deg	7.763
r_long_range_B_refined	6.133
r_long_range_B_other	6.127
r_mcangle_other	2.407
r_mcangle_it	2.406
r_scangle_other	2.325
r_angle_refined_deg	1.849
r_mcbond_it	1.427
r_mcbond_other	1.424
r_scbond_it	1.409
r_scbond_other	1.409
r_angle_other_deg	0.969
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3132
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing