Experiment: 3TKU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VD5	PDB ENTRY 2VD5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	10-20% PEG 3350, 0.1 M BISTRIS, 0.1 M SODIUM TARTRATE, 0.1 M AMMONIUM SULPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, VAPOR DIFFUSION, SITTING DROP, pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.95	α = 90
b = 123.52	β = 101.13
c = 84.77	γ = 90

Symmetry
Space Group	P 1 21 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		2009-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92	Diamond	I04

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	2.15	49.59	97.1	0.116			47854	45515	2	2

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	2.15	2.21	84.3		0.467

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 ENTRY 2VD5	2.15	40	1	47854	45515	2412	97.3	0.223	0.221	0.273	RANDOM	40.216

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]
-1.58		0.8	-1.55		3.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.678
r_dihedral_angle_3_deg	18.052
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_1_deg	7.056
r_scangle_it	4.499
r_scbond_it	2.895
r_angle_refined_deg	2.009
r_mcangle_it	1.793
r_mcbond_it	0.983
r_chiral_restr	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.678
r_dihedral_angle_3_deg	18.052
r_dihedral_angle_4_deg	17.948
r_dihedral_angle_1_deg	7.056
r_scangle_it	4.499
r_scbond_it	2.895
r_angle_refined_deg	2.009
r_mcangle_it	1.793
r_mcbond_it	0.983
r_chiral_restr	0.136
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6225
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	88

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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 R01GM157729.