7A9G

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis with intermediate 2-acetyl-thiamine diphosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M DL-Malic acid, MES monohydrate, Tris (MMT)-buffer, pH 5.0 + 25% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.865	α = 90
b = 126.17	β = 106.285
c = 79.031	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	PIXEL	DECTRIS PILATUS 6M-F	double crystal monochromator	2017-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033213	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	1.9	48.552	99.39	0.04858	0.04858	0.997	12.4	1.9		92339

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.968	99.38		0.3653	0.3653	0.779	2.52	1.9

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	2o1x	1.9	48.552	92339	971	99.348	0.154	0.1539	0.1904	22.378

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]
0.213		-0.301	1.789		-1.559

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.044
r_dihedral_angle_4_deg	14.097
r_dihedral_angle_3_deg	13.567
r_dihedral_angle_1_deg	6.328
r_lrange_it	4.927
r_lrange_other	4.912
r_scangle_it	3.76
r_scangle_other	3.76
r_scbond_it	2.457
r_scbond_other	2.456
r_mcangle_it	2.371
r_mcangle_other	2.371
r_angle_other_deg	2.331
r_mcbond_it	1.621
r_mcbond_other	1.615
r_angle_refined_deg	1.476
r_nbd_other	0.273
r_symmetry_nbd_refined	0.257
r_symmetry_nbd_other	0.217
r_nbd_refined	0.205
r_nbtor_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.15
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.072
r_symmetry_nbtor_other	0.072
r_bond_other_d	0.035
r_symmetry_xyhbond_nbd_other	0.031
r_gen_planes_other	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8125
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	220

Software

Software
Software Name	Purpose
REFMAC	refinement
pointless	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building