Experiment: 3FXT

Crystal structure of the N-terminal domain of human NUDT6

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	19% PEG2000 MME, 0.1M Tris-HCl, 0.25M Trimethylamine. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2	VAPOR DIFFUSION, HANGING DROP	7.5	277	19% PEG2000 MME, 0.1M Tris-HCl, 0.3M Trimethylamine. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100. Crystal was then soaked for 17h in 10% PEG 2000MME, 0.1M Tris-HCl, 0.3M Trimethylamine and 1mM HgAc., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
3	VAPOR DIFFUSION, HANGING DROP	7.5	277	14% PEG2000 MME, 0.1M Tris-HCl. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100. Crystal was then soaked for 2weeks 10% PEG 2000MME, 0.1M Tris-HCl, 0.3M Trimethylamine and 1mM SmCl3., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.8	α = 90
b = 185.8	β = 90
c = 129.2	γ = 120

Symmetry
Space Group	P 64 2 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	ADSC QUANTUM Q315r	MIRRORS	2008-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97931	ESRF	ID29

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	2.3		99.5	0.091	0.115	17.09	7.05	58581	58279		-3

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)
1	2.3	2.36	99.1		0.757	0.658	3.08	6.66	4241

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	2.3	33.88	-3	55426	55426	2957	100	0.20286	0.20286	0.20112	0.2266	0.23539	0.2623	RANDOM	11.082

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]
0.17	0.09		0.17		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.02
r_dihedral_angle_4_deg	14.784
r_dihedral_angle_3_deg	13.92
r_dihedral_angle_1_deg	5.275
r_angle_other_deg	2.199
r_scangle_it	2.039
r_scbond_it	1.157
r_angle_refined_deg	1.022
r_mcangle_it	0.998
r_mcbond_it	0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.02
r_dihedral_angle_4_deg	14.784
r_dihedral_angle_3_deg	13.92
r_dihedral_angle_1_deg	5.275
r_angle_other_deg	2.199
r_scangle_it	2.039
r_scbond_it	1.157
r_angle_refined_deg	1.022
r_mcangle_it	0.998
r_mcbond_it	0.52
r_chiral_restr	0.062
r_mcbond_other	0.033
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5594
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	36

Software

Software
Software Name	Purpose
ADSC	data collection
autoSHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling