6OEW | pdb_00006oew

Structure of a Cytidylyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Molecular Dimensions Morpheus screen, a6: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30mM of each magnesium chloride and calcium chloride, 100mM MOPS/HEPES-Na pH 7.5: LpboA.19557.c.B1.PS38542 at 24.74mg/ml: cryo: direct: tray 306886 a6: puck ogn0-8. For experimental phasing, a crystal from Morpheus screen a3 (10% w/v PEG 4000, 20% v/v glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM MES/imidazole pH 6.5: LpboA.19557.c.B1.PS38542 at 24.74mg/ml) was incubated for 20sec in a solution of 92.5% reservoir and 7.5% 5M Sodium iodide in ethylene glycol, and vitrified: tray: 306886 a3: puck: kzx0-4

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.51	α = 90
b = 65.51	β = 90
c = 261.93	γ = 90

Symmetry
Space Group	P 43 21 2

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	RAYONIX MX-300		2019-02-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2019-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F
2	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	1.85	43.671	100	0.054	0.057	0.999	22.16	9.57		50144			38.04

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	1.85	1.9	100		0.581	0.614	0.954	3.27	9.747

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.85	43.671	1.35	49962	1946	99.86	0.1731	0.1714	0.17	0.2147	0.21	0	41.3441

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	15.228
f_angle_d	0.989
f_chiral_restr	0.06
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3860
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	28

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PARROT	phasing
ARP/wARP	model building
BUCCANEER	model building
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.