7B65 | pdb_00007b65

Structure of NUDT15 R139C Mutant in complex with TH7755

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LPG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.12 M Monosaccharide mix (Morpheus Screen) 0.1 M Imidazole/MES pH 6,5, 12.5% MPD, 12.5% PEG 1000, 12.5 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.91	α = 91.582
b = 43.803	β = 106.74
c = 60.457	γ = 113.478

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 EIGER X 16M		2019-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.97622	MAX IV	BioMAX

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	1.6	35.37	96.6	0.997	16.2	3.6		39574

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	1.6	1.63			0.985

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5LPG	1.6	35.37	39573	1981	96.595	0.161	0.1597	0.17	0.1843	0.19	21.914

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]
0.797	0.265	-0.433	0.964	-0.403	-1.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.615
r_dihedral_angle_3_deg	13.002
r_dihedral_angle_4_deg	9.987
r_dihedral_angle_1_deg	7.111
r_lrange_it	6.506
r_lrange_other	6.397
r_scangle_it	5.196
r_scangle_other	5.194
r_scbond_it	3.405
r_scbond_other	3.404
r_mcangle_it	3.023
r_mcangle_other	3.023
r_mcbond_it	2.127
r_mcbond_other	2.123
r_angle_refined_deg	1.886
r_angle_other_deg	1.497
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.209
r_symmetry_nbd_refined	0.207
r_nbd_other	0.199
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.12
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2472
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	64

Software

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