Experiment: 8OSC

Structure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) bound to deoxyuridine 5'- monophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		model obtained after solving apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293.15	[40 mM sodium propionate, 20 mM MES and 40 mM BIS-TRIS propane] pH 4.0 and 20% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.354	α = 90
b = 38.772	β = 120.29
c = 66.195	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER2 XE 16M		2022-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.42	33.38	99.7	0.058	0.06	0.015	0.999	24.7	15.4		44559			19.39

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44	94.9		0.814	0.855	0.254	0.899	4	10.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.42	33.38	1.41	44541	2299	99.64	0.1979	0.1972	0.1993	0.2104	0.2084

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.603
f_angle_d	0.941
f_chiral_restr	0.078
f_plane_restr	0.009
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1951
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	20

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing