8QHQ

Crystal structure of human DNPH1 bound to hmdUMP

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-04-23
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.9763
Spacegroup name	P 1 21 1
Unit cell lengths	56.648, 67.126, 120.117
Unit cell angles	90.00, 99.63, 90.00

Refinement procedure

Resolution	55.850 - 1.780
R-factor	0.2066
Rwork	0.206
R-free	0.22440
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.560
Data reduction software	XDS (Feb 5, 2021)
Data scaling software	pointless (1.12.8)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	59.212	1.806
High resolution limit [Å]	1.775	1.775
Rmerge	0.125
Rmeas	0.132
Rpim	0.042
Number of reflections	80370	3316
<I/σ(I)>	11.7
Completeness [%]	93.5
Redundancy	9.5
CC(1/2)	0.999	0.398

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M sodium fluoride, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350