7R0D

Structure of NUDT15 in complex with Geranyl monophosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.1 M Tris pH 8.5, 0.2 M sodium acetate, 30 % PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.642	α = 90
b = 48.269	β = 90
c = 135.197	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.7	46.64	99.7	0.998	17.8	11.3		34417

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			0.9

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5LPG	1.7	45.5	34343	1722	99.64	0.186	0.1841	0.2263	27.836

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]
-0.551			2.346		-1.795

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.385
r_dihedral_angle_4_deg	16.083
r_dihedral_angle_3_deg	15.891
r_lrange_it	7.444
r_lrange_other	7.434
r_dihedral_angle_1_deg	7.03
r_scangle_it	5.837
r_scangle_other	5.835
r_scbond_it	3.795
r_scbond_other	3.788
r_mcangle_other	3.368
r_mcangle_it	3.366
r_mcbond_it	2.523
r_mcbond_other	2.517
r_angle_refined_deg	1.715
r_angle_other_deg	1.432
r_nbd_refined	0.216
r_symmetry_nbd_other	0.187
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.156
r_symmetry_nbd_refined	0.125
r_symmetry_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.081
r_metal_ion_refined	0.06
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2471
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	32

Software

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