7VZ6

The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in complex with UDP-glucose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.2M lithium sulfate, 0.1M Bis tris pH 5.5, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.833	α = 74.867
b = 104.941	β = 72.918
c = 106.84	γ = 68.076

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	CCD	RAYONIX MX300HE		2019-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.09	21.56	95.2	0.057	19.7	2.2		176474

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18			0.057

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	NONE	1vgv	2.092	21.558	176474	8824	95.09	0.202	0.2008	0.2278	28.96

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]
0.119	0.018	0.108	0.052	0.02	-0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.758
r_dihedral_angle_4_deg	15.456
r_dihedral_angle_3_deg	15.3
r_lrange_it	7.12
r_lrange_other	7.077
r_dihedral_angle_1_deg	6.585
r_scangle_it	5.225
r_scangle_other	5.225
r_mcangle_other	3.75
r_mcangle_it	3.749
r_scbond_it	3.305
r_scbond_other	3.305
r_mcbond_it	2.532
r_mcbond_other	2.53
r_angle_other_deg	1.558
r_angle_refined_deg	1.495
r_symmetry_nbd_refined	0.211
r_nbd_other	0.209
r_nbd_refined	0.203
r_symmetry_nbd_other	0.2
r_xyhbond_nbd_refined	0.181
r_metal_ion_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.148
r_ncsr_local_group_13	0.09
r_ncsr_local_group_8	0.088
r_ncsr_local_group_11	0.088
r_ncsr_local_group_22	0.087
r_ncsr_local_group_9	0.086
r_ncsr_local_group_20	0.086
r_ncsr_local_group_18	0.085
r_ncsr_local_group_7	0.084
r_ncsr_local_group_1	0.083
r_ncsr_local_group_10	0.083
r_ncsr_local_group_12	0.081
r_ncsr_local_group_28	0.081
r_ncsr_local_group_14	0.08
r_ncsr_local_group_5	0.079
r_ncsr_local_group_19	0.078
r_ncsr_local_group_25	0.078
r_ncsr_local_group_27	0.077
r_ncsr_local_group_3	0.076
r_chiral_restr	0.074
r_ncsr_local_group_21	0.074
r_ncsr_local_group_15	0.073
r_ncsr_local_group_23	0.073
r_ncsr_local_group_2	0.072
r_ncsr_local_group_16	0.072
r_ncsr_local_group_24	0.072
r_ncsr_local_group_17	0.071
r_symmetry_xyhbond_nbd_other	0.07
r_ncsr_local_group_26	0.069
r_ncsr_local_group_4	0.068
r_ncsr_local_group_6	0.068
r_symmetry_nbtor_other	0.067
r_bond_other_d	0.018
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22403
Nucleic Acid Atoms
Solvent Atoms	1499
Heterogen Atoms	295

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing