7A9H

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O1X

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
2.32	47.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.987	α = 108.956
b = 76.1	β = 106.53
c = 79.148	γ = 107.594

Symmetry
Space Group	P 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	2017-12-03	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	1.849	43.832	91	0.0233	0.0233	0.999	20.99	1.8		93268

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	1.85	1.916	62.53		0.0852	0.0852	0.979	6.54	1.7

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	2o1x	1.849	43.832	93268	2101	90.85	0.151	0.1507	0.1736	19.252

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]
-0.044	0.233	-0.22	0.678	0.079	-0.432

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.325
r_dihedral_angle_4_deg	14.616
r_dihedral_angle_3_deg	13.088
r_dihedral_angle_1_deg	6.254
r_lrange_it	4.36
r_lrange_other	4.36
r_scangle_it	2.864
r_scangle_other	2.863
r_angle_other_deg	2.358
r_mcangle_it	2.039
r_mcangle_other	2.038
r_scbond_other	1.805
r_scbond_it	1.804
r_angle_refined_deg	1.37
r_mcbond_it	1.318
r_mcbond_other	1.314
r_nbd_other	0.223
r_symmetry_nbd_other	0.213
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.152
r_symmetry_nbd_refined	0.147
r_xyhbond_nbd_refined	0.122
r_symmetry_xyhbond_nbd_other	0.085
r_chiral_restr	0.068
r_symmetry_nbtor_other	0.063
r_bond_other_d	0.035
r_gen_planes_other	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8162
Nucleic Acid Atoms
Solvent Atoms	666
Heterogen Atoms	54

Software

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