7PVI

dTDP-sugar epimerase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	1.0 M sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate pH 6.5) Crystal was soaked in 15% w/v of D-xylose

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.033	α = 90
b = 84.539	β = 113.592
c = 77.673	γ = 90

Symmetry
Space Group	C 1 2 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		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.434	51.39	65.9	0.999	12.5	3.3		54843

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	1.434	1.605			0.585

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	2IXI	1.434	51.39	54843	2739	65.738	0.168	0.1667	0.1986	21.918

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]
0.025		-0.013	0.033		-0.034

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.163
r_dihedral_angle_4_deg	15.384
r_dihedral_angle_3_deg	15.065
r_dihedral_angle_1_deg	7.172
r_lrange_it	6.745
r_lrange_other	6.56
r_scangle_it	3.824
r_scangle_other	3.824
r_mcangle_it	3.225
r_mcangle_other	3.2
r_scbond_other	2.531
r_scbond_it	2.53
r_mcbond_it	2.072
r_mcbond_other	2.031
r_angle_refined_deg	1.453
r_angle_other_deg	1.393
r_metal_ion_refined	0.359
r_nbd_other	0.298
r_symmetry_nbd_refined	0.28
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_refined	0.217
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.161
r_ncsr_local_group_1	0.12
r_xyhbond_nbd_other	0.114
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.035
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3198
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data reduction
autoPROC	data processing
MoRDa	phasing
STARANISO	data scaling