24OK | pdb_000024ok

Crystal structure of human dUTPase complexed with Zinc.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5H4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystal condition: 0.09M 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol. 0.1M Tris (base), BICINE. 30% v/v Glycerol, PEG 4000. (Morpheus D3) Seeded with: 0.2M Zinc Acetate, 0.1M Sodium cacodylate, 10% v/v 2-Propanol, pH 6.5 (JCSG E7)

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.253	α = 90
b = 84.253	β = 90
c = 84.253	γ = 90

Symmetry
Space Group	P 21 3

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		2024-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	2.01	48.691	100	0.998	19.5	19.4		13576

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	2.01	2.06			0.431	1.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.01	48.691	13553	662	99.97	0.213	0.2122	0.2147	0.2335	0.2285	RANDOM	51.567

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
r_dihedral_angle_3_deg	13.173
r_dihedral_angle_6_deg	11.639
r_lrange_it	9.809
r_lrange_other	9.798
r_scangle_it	7.547
r_scangle_other	7.542
r_dihedral_angle_2_deg	6.674
r_dihedral_angle_1_deg	6.222
r_mcangle_it	6.007
r_mcangle_other	6.003
r_scbond_it	5.044
r_scbond_other	5.039
r_mcbond_it	4.247
r_mcbond_other	4.24
r_angle_refined_deg	1.297
r_angle_other_deg	1.248
r_nbd_other	0.329
r_symmetry_nbd_other	0.214
r_symmetry_nbd_refined	0.2
r_nbd_refined	0.19
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.088
r_symmetry_metal_ion_refined	0.081
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.025
r_gen_planes_other	0.019
r_gen_planes_refined	0.01
r_bond_refined_d	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	943
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	17

Software

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