8RDZ | pdb_00008rdz

Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with Ibrutinib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Apo structure solved

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Tris, PEG4K, magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.71	α = 80.652
b = 59.2	β = 82.958
c = 79.431	γ = 77.028

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M		2019-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.920	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.02	49.56	96.87	0.05739	0.07063	0.04047	0.994	7.35	2.8		53078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.092			0.8753	0.243

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.02	49.557	52925	2657	96.943	0.224	0.2207	0.23	0.289	0.29	45.269

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]
2.076	1.454	2.016	-0.918	1.351	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.934
r_dihedral_angle_3_deg	14.436
r_dihedral_angle_6_deg	13.677
r_lrange_other	9.312
r_lrange_it	9.31
r_dihedral_angle_1_deg	7.878
r_scangle_it	7.107
r_scangle_other	7.106
r_mcangle_it	6.472
r_mcangle_other	6.471
r_scbond_it	4.837
r_scbond_other	4.836
r_mcbond_it	4.603
r_mcbond_other	4.601
r_dihedral_angle_other_2_deg	1.89
r_angle_refined_deg	1.773
r_angle_other_deg	0.584
r_nbd_refined	0.22
r_symmetry_nbd_other	0.197
r_symmetry_nbd_refined	0.183
r_nbtor_refined	0.18
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.12
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_refined	0.061
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5894
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	168

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
XDS	data scaling