Experiment: 9OBB

Crystal structure of dihydroorotate dehydrogenase from Leishmania brasiliensis in complex with 5-[(E)-3-(p-methoxyphenyl)-2-propenylidene]-2,4,6(1H,3H,5H)-pyrimidinetrione

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WZH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	294.15	0.6-1.6 M ammonium sulfate, 0.25-1 M lithium sulfate, 0.1 M sodium citrate (pH 5.6).

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.644	α = 90
b = 104.595	β = 90
c = 106.609	γ = 90

Symmetry
Space Group	P 21 21 21

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 2M		2024-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRIUS BEAMLINE MANACA	0.97714	LNLS SIRIUS	MANACA

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	2.32	47.54	99.8	0.993	7.94	11.2		30574			43.67

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	2.32	2.46			0.434	1.09

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.32	47.54	1.34	30574	1998	99.79	0.1973	0.194	0.1962	0.2452	0.2466	45.57

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	11.3116
f_angle_d	0.8962
f_chiral_restr	0.0555
f_bond_d	0.0085
f_plane_restr	0.0064

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4568
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	62

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHENIX	phasing
Coot	model building