3PNW

Crystal Structure of the tudor domain of human TDRD3 in complex with an anti-TDRD3 FAB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HFF	pdb entries 2HFF (modified on FFAS03 server) and 3PMT
experimental model	PDB	3PMT	pdb entries 2HFF (modified on FFAS03 server) and 3PMT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	16% PEG-3350, 0.05M citric acid, 0.05M bis-tris propane, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.708	α = 80.96
b = 93.726	β = 82.82
c = 159.932	γ = 90.06

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	CCD	ADSC QUANTUM 315		2010-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97924	APS	19-ID

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	2.05	50	97.4	0.086	6.4	2.5		266201

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	2.05	2.12	93.1		0.414		2.3	25457

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	pdb entries 2HFF (modified on FFAS03 server) and 3PMT	2.05	30	266095	2162	97.202	0.224	0.2233	0.2635	thin shells (SFTOOLS)	45.03

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]
-1.951	-0.248	0.076	0.537	-2.489	2.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.294
r_dihedral_angle_4_deg	19.749
r_dihedral_angle_3_deg	13.334
r_dihedral_angle_1_deg	7.101
r_scangle_it	3.16
r_scbond_it	2.03
r_mcangle_it	1.338
r_angle_refined_deg	1.267
r_angle_other_deg	0.879
r_mcbond_it	0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.294
r_dihedral_angle_4_deg	19.749
r_dihedral_angle_3_deg	13.334
r_dihedral_angle_1_deg	7.101
r_scangle_it	3.16
r_scbond_it	2.03
r_mcangle_it	1.338
r_angle_refined_deg	1.267
r_angle_other_deg	0.879
r_mcbond_it	0.76
r_mcbond_other	0.175
r_chiral_restr	0.078
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29516
Nucleic Acid Atoms
Solvent Atoms	1275
Heterogen Atoms	143

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.