7MYD

Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile

X-RAY DIFFRACTION

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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		295	100 mM sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.071	α = 90
b = 143.071	β = 90
c = 68.997	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		2011-04-15	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	2.15	35.77	97.8	0.137	0.137	11.9	7		43015

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	2.15	2.27	98.1		0.803	0.803	2.6	6.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 3GYE	2.15	35.77	43011	2164	97.852	0.18	0.1781	0.2187	26.369

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]
-0.055	-0.028		-0.055		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.423
r_dihedral_angle_4_deg	16.64
r_dihedral_angle_3_deg	13.042
r_dihedral_angle_1_deg	7.394
r_lrange_it	3.964
r_lrange_other	3.928
r_scangle_it	2.763
r_scangle_other	2.762
r_mcangle_other	2.218
r_mcangle_it	2.217
r_scbond_it	1.724
r_scbond_other	1.723
r_mcbond_it	1.421
r_mcbond_other	1.415
r_angle_refined_deg	1.314
r_angle_other_deg	1.273
r_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.188
r_symmetry_nbd_refined	0.174
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.153
r_symmetry_xyhbond_nbd_other	0.087
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4612
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	109

Software

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