6MAO | pdb_00006mao

Crystal structure of Deoxyuridine 5'-triphosphate nucleotidohydrolase from Legionella pneumophila Philadelphia 1 in complex with dUMP (Deoxyuridine 5'-monophosphate)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MAI	apo structure, 6MAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	285	Molecular Dimensions Morpheus screen, condition C4: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 30mM each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MES/imidazole pH 6.5: LepnA.01206.a.B1.PS38438 at 24.33mg/ml: 2h soak with 5mM MgCl2 + dUTP with was converted to dUMP: cryo: direct: EG in two steps: tray 301633a1, puck PXP9-8

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.67	α = 90
b = 85.67	β = 90
c = 55.46	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	CCD	RIGAKU SATURN 944+		2018-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.95	37.096	100	0.059	0.063	0.999	22.98	9.282		17033			34.444

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	99.9		0.47	0.523	0.878	3.04	5.22

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	apo structure, 6MAI	1.95	37.096	1.35	17031	1774	99.97	0.1515	0.1482	0.15	0.1811	0.18	34.5277

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	13.83
f_angle_d	0.933
f_chiral_restr	0.074
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1044
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	33

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.