Experiment: 6ULO

Structure of an N-terminally truncated uncharacterized protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	290	Molecular Dimensions Morpheus screen, condition H5: 10% w/v PEG 20 000, 20% v/v PEG MME 550: 20mM of each amino acid: sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MOPS/HEPES-Na pH 7.5: LpinA.195645.a.B2.PW386228 at 23mg/ml. Cryo: direct: tray 310523 h5: puck PAS1-8. For phasing a crystal from the same tray, well C1 (10% w/v PEG 20 000, 20% v/v PEG MME 550: 30mM of each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MES/imidazole pH 6.5) was incubated for 20sec in a mixture of 10% 5M sodium iodide in ethylene glycol (500mM final NaI concentration) and 90% reservoir solution. Diffraction data were collected in-house.Tray 310523 c1: puck LOF7-9

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.44	α = 98.637
b = 56.65	β = 106.327
c = 60.99	γ = 83.326

Symmetry
Space Group	P 1

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		2019-08-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2019-09-20	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	1.3	50	95.3	0.036	0.041	1	19.58	3.927		155840			19.615

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	1.3	1.33	92.6		0.557	0.645	0.835	2.35	3.953

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	FREE R-VALUE	1.3	32.24	1.98	155816	1916	95.39	0.138	0.1375	0.1375	0.1722	0.1722	0	19.46

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	14.3364
f_angle_d	1.1122
f_chiral_restr	0.0849
f_bond_d	0.0093
f_plane_restr	0.0071

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4926
Nucleic Acid Atoms
Solvent Atoms	1021
Heterogen Atoms	2

Software

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