Experiment: 2IKF

Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B51	PDB entry 2B51

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 18% PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.773	α = 90
b = 41.525	β = 94.94
c = 103.792	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.979	ALS	4.2.2

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	2	103.407	94.5	0.098	0.098	6.3	3		43289

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.11	95.6		0.573	0.573	0.8	2.9	6344

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 2B51	2	51.709	43270	2222	94.3	0.228	0.2265	0.275	0.2745	36.984

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]
0.746		0.28	-0.915		0.169

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.249
c_mcangle_it	2.38
c_scbond_it	2.26
c_angle_deg	1.777
c_mcbond_it	1.502
c_bond_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5087
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
CCP4	data scaling
PHASER	phasing