6XXG

Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.2 M Calcium acetate hydrate, 0.1 M Tris, 20 % PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.321	α = 90
b = 87.367	β = 90
c = 181.865	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 PILATUS 6M-F		2017-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.099	47.549	99.08	0.913	5.87	2		67987

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.175	99.48		0.444

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	2.099	47.549	67497	3427	98.976	0.193	0.1908	0.236	28.734

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]
-0.023			0.007		0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.139
r_dihedral_angle_4_deg	15.213
r_dihedral_angle_3_deg	14.664
r_dihedral_angle_1_deg	6.396
r_lrange_it	5.23
r_lrange_other	5.198
r_scangle_it	3.444
r_scangle_other	3.443
r_mcangle_it	2.69
r_mcangle_other	2.69
r_angle_other_deg	2.343
r_scbond_it	2.093
r_scbond_other	2.089
r_mcbond_it	1.698
r_mcbond_other	1.697
r_angle_refined_deg	1.402
r_metal_ion_refined	0.246
r_symmetry_nbd_refined	0.221
r_symmetry_nbd_other	0.211
r_nbd_other	0.21
r_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.157
r_nbtor_refined	0.149
r_symmetry_nbtor_other	0.064
r_chiral_restr	0.062
r_bond_other_d	0.036
r_gen_planes_other	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8274
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	63

Software

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