3BEO | pdb_00003beo

A Structural Basis for the allosteric regulation of non-hydrolyzing UDP-GlcNAc 2-epimerases

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Hanging drop	8.5	277	PEG 4000-6000, 100mM Tris-HCl, 0.2M Li2SO4, pH 8.5, Hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.404	α = 90
b = 188.165	β = 112.22
c = 61.679	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.7	60	99.4	0.087			107005	107005	0.001	0.001

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.74	99		0.346	0.346	3.4	3.4	7332

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.7	43.03	106401	5305	99.43	0.223	0.221	0.23	0.262	0.26	RANDOM	12.67

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]
-0.47		-0.12	0.4		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.848
r_dihedral_angle_4_deg	15.883
r_dihedral_angle_3_deg	12.505
r_dihedral_angle_1_deg	6.217
r_scangle_it	4.36
r_scbond_it	3.352
r_mcangle_it	2.011
r_angle_refined_deg	1.757
r_mcbond_it	1.671
r_angle_other_deg	1.09
r_mcbond_other	0.801
r_symmetry_vdw_other	0.352
r_symmetry_hbond_refined	0.313
r_symmetry_vdw_refined	0.27
r_xyhbond_nbd_refined	0.229
r_nbd_refined	0.216
r_nbd_other	0.21
r_nbtor_refined	0.167
r_chiral_restr	0.114
r_nbtor_other	0.086
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5896
Nucleic Acid Atoms
Solvent Atoms	577
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction