8RIY

Human NUDT5 with ibrutinib derivative

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.2 M ammonium acetate, 0.1 M citrate pH 5.5, 30 % PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.605	α = 90
b = 60.605	β = 90
c = 502.608	γ = 120

Symmetry
Space Group	P 61 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	PIXEL	DECTRIS EIGER X 4M		2022-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	2.288	83.768	85.8	0.335	10.3	35.1		9387

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	2.288	2.646			2.541	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.288	83.768	9387	450	35.535	0.229	0.2255	0.2948	44.38

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]
0.518	0.259		0.518		-1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.396
r_dihedral_angle_3_deg	17.443
r_dihedral_angle_4_deg	16.452
r_lrange_it	7.152
r_lrange_other	7.148
r_dihedral_angle_1_deg	7.027
r_mcangle_it	4.602
r_mcangle_other	4.601
r_scangle_it	4.014
r_scangle_other	4.013
r_mcbond_it	2.722
r_mcbond_other	2.716
r_scbond_it	2.337
r_scbond_other	2.337
r_angle_refined_deg	1.374
r_angle_other_deg	1.14
r_symmetry_xyhbond_nbd_refined	0.221
r_nbd_refined	0.2
r_nbd_other	0.195
r_xyhbond_nbd_refined	0.182
r_symmetry_nbd_other	0.18
r_symmetry_nbd_refined	0.173
r_nbtor_refined	0.155
r_ncsr_local_group_1	0.122
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.045
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_symmetry_xyhbond_nbd_other	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2922
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	60

Software

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