2AF6 | pdb_00002af6

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O26	PDB ENTRY 1O26

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	100mM Sodium acetate, 200mM potassium iodide, 2mM DTT and PEG3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.09	α = 90
b = 78.3	β = 96.8
c = 168.72	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210		2004-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9794	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.013	44.95	96.1	0.096	11.4	3.4	132869	132869			20.73

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	89		0.474	3.1	2.9	12213

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 in combination with Molecular Replacement	THROUGHOUT	PDB ENTRY 1O26	2.01	44.95	132869	126330	6506	95.47	0.1978	0.1978	0.19548	0.2	0.24292	0.24	RANDOM	24.695

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	31.286
r_dihedral_angle_4_deg	18.014
r_dihedral_angle_3_deg	14.934
r_dihedral_angle_1_deg	5.441
r_scangle_it	2.568
r_scbond_it	1.667
r_angle_refined_deg	1.293
r_mcangle_it	1.139
r_mcbond_it	0.681
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.286
r_dihedral_angle_4_deg	18.014
r_dihedral_angle_3_deg	14.934
r_dihedral_angle_1_deg	5.441
r_scangle_it	2.568
r_scbond_it	1.667
r_angle_refined_deg	1.293
r_mcangle_it	1.139
r_mcbond_it	0.681
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.286
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.16
r_metal_ion_refined	0.126
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15074
Nucleic Acid Atoms
Solvent Atoms	989
Heterogen Atoms	686

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
AMoRE	phasing

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.