8PTT | pdb_00008ptt

Human NUDT5 in complex with MRK-952

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished NUDT5 structure solved in the lab

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	Reservoir: 33% PEG 400, 0.2 M magnesium chloride, and 0.1 M tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.245	α = 78.789
b = 59.679	β = 81.715
c = 81.171	γ = 76.034

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		2021-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	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	2.5	28.41	98.4	0.051	9.2	3.2		29822			33.048

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	2.5	2.6	97.9		0.225	2.9	3.5

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	THROUGHOUT	2.5	28.41	29822	1433	98.439	0.181	0.178	0.18	0.2453	0.24	39.036

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]
2.431	0.788	0.886	-0.257	0.678	-1.241

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.43
r_dihedral_angle_6_deg	12.941
r_dihedral_angle_2_deg	7.804
r_dihedral_angle_1_deg	6.731
r_lrange_it	4.989
r_lrange_other	4.969
r_mcangle_it	2.856
r_mcangle_other	2.855
r_scangle_it	2.825
r_scangle_other	2.825
r_mcbond_it	1.663
r_mcbond_other	1.662
r_scbond_it	1.625
r_scbond_other	1.625
r_angle_refined_deg	1.226
r_angle_other_deg	0.289
r_chiral_restr	0.232
r_nbd_refined	0.186
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.166
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.125
r_symmetry_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	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	6062
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	127

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement