8K6W

dUTPase of helicobacter pylori 26695

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MBQ	3MBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	MORPHEUS H4 condition:0.1 M Amino acid mix, 0.1 M buffer system pH 6.5, 50% V/V precipitant mix 4

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.36	α = 90
b = 102.36	β = 90
c = 78.37	γ = 120

Symmetry
Space Group	P 63

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 PILATUS 6M		2018-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9791	ESRF	ID30B

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	2.5	58.7	100	0.99	18.7	46.3		16291

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	2.5	2.6			0.833

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3MBQ	2.5	58.7	16273	1092	99.969	0.179	0.175	0.2384	47.122

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]
-0.165	-0.082		-0.165		0.535

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.384
r_dihedral_angle_6_deg	15.109
r_lrange_other	7.5
r_lrange_it	7.497
r_dihedral_angle_1_deg	7.184
r_dihedral_angle_2_deg	6.519
r_scangle_it	5.812
r_scangle_other	5.81
r_mcangle_it	3.954
r_mcangle_other	3.954
r_scbond_it	3.605
r_scbond_other	3.589
r_mcbond_it	2.53
r_mcbond_other	2.513
r_angle_refined_deg	1.339
r_angle_other_deg	0.447
r_symmetry_nbd_refined	0.389
r_symmetry_xyhbond_nbd_refined	0.346
r_nbd_other	0.245
r_nbd_refined	0.203
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2981
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms

Software

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