3MHU

Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with 5-Nitroorotic acid

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	0.1M sodium citrate tribasic dihydrate pH 5.6, 1.1M lithium sulfate, 0.45M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.562	α = 90
b = 141.562	β = 90
c = 68.811	γ = 120

Symmetry
Space Group	P 61

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	MAR CCD 165 mm		2009-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.437	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	31.47	97.6	0.085	0.085	14.9	6.3		65142		2.5	20.54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.85	1.95	98.8		0.552	0.552	2.7	6	9593

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3GYE	1.85	31.47	61820	3295	96.95	0.15995	0.15815	0.19397	RANDOM	20.691

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
r_dihedral_angle_2_deg	40.215
r_dihedral_angle_4_deg	14.845
r_dihedral_angle_3_deg	13.303
r_dihedral_angle_1_deg	6.366
r_scangle_it	5.76
r_scbond_it	4.033
r_mcangle_it	2.391
r_mcbond_it	1.542
r_angle_refined_deg	1.248
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.215
r_dihedral_angle_4_deg	14.845
r_dihedral_angle_3_deg	13.303
r_dihedral_angle_1_deg	6.366
r_scangle_it	5.76
r_scbond_it	4.033
r_mcangle_it	2.391
r_mcbond_it	1.542
r_angle_refined_deg	1.248
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4645
Nucleic Acid Atoms
Solvent Atoms	580
Heterogen Atoms	125

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.