8QLD

Bacteriophage T5 dUTPase mutant with loop deletion (30-35 aa)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QKY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	296	0.085 M HEPES sodium, 1.7% v/v Polyethylene glycol 400, 1.7 M Ammonium sulfate, 15% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.726	α = 90
b = 88.726	β = 90
c = 99.999	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	RIGAKU HyPix-6000HE		2023-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	23	99.1	0.094	0.998	13.4	9		26147

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.51	0.954	3.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	20.001	24792	1160	94.905	0.223	0.2206	0.2641	31.508

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]
-0.232	-0.116		-0.232		0.754

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.02
r_dihedral_angle_6_deg	16.549
r_dihedral_angle_1_deg	6.694
r_dihedral_angle_2_deg	6.668
r_lrange_it	4.384
r_lrange_other	4.302
r_scangle_it	2.656
r_scangle_other	2.466
r_mcangle_it	1.938
r_mcangle_other	1.938
r_scbond_it	1.72
r_scbond_other	1.561
r_angle_refined_deg	1.342
r_mcbond_it	1.21
r_mcbond_other	1.21
r_angle_other_deg	0.461
r_nbd_other	0.221
r_symmetry_nbd_other	0.205
r_nbd_refined	0.193
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.144
r_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.068
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3045
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	39

Software

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