8OFW

Crystal structure of the full-length dihydroorotate dehydrogenase from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	P9WHL1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293.15	0,2 M Sodium Chloride, 0,1 M Tris-HCl pH 8,5 and 25 % (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.05	α = 90
b = 85.215	β = 90
c = 181.005	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 PILATUS3 2M		2022-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

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	3.8	41.508	97.5	0.253	0.279	0.988	5	5.5		39498			116.1

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	3.8	4			1.229	1.358	0.688	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.8	41.508	7194	354	95.869	0.259	0.2551	0.3278	125.462

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]
-1.45			16.102		-14.653

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	27.768
r_lrange_other	27.768
r_mcangle_it	16.315
r_mcangle_other	16.314
r_scangle_it	15.707
r_scangle_other	15.705
r_dihedral_angle_3_deg	13.637
r_dihedral_angle_6_deg	11.238
r_mcbond_it	9.83
r_mcbond_other	9.83
r_scbond_it	9.232
r_scbond_other	9.23
r_dihedral_angle_1_deg	5.356
r_dihedral_angle_2_deg	2.976
r_angle_refined_deg	0.974
r_angle_other_deg	0.343
r_symmetry_xyhbond_nbd_refined	0.271
r_nbd_other	0.26
r_symmetry_nbd_refined	0.244
r_symmetry_nbd_other	0.212
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.172
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.073
r_chiral_restr	0.049
r_chiral_restr_other	0.013
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5192
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing