8P20 | pdb_00008p20

TarM(Se)_G117R-UDP-4RboP-glucose

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293	10% PEG 20 000, 25% PEG MME 550, 0.1 M MES/imidazole, pH 6.9, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium tartrate (racemic), 0.02 M sodium oxamate.

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.62	α = 90.015
b = 75.75	β = 90.039
c = 129.4	γ = 90.031

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 2M		2020-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9998671568878699	SLS	X06DA

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	2.848	49.23	99.9	0.99	5.8	4.6		51972

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	2.848	2.92	100		0.41

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MIR	FREE R-VALUE	2.848	49.204	51971	2691	99.752	0.23	0.2283	0.23	0.2664	0.27	48.793

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]
-13.915	15.052	-5.92	55.116	31.486	-41.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.622
r_dihedral_angle_3_deg	22.562
r_dihedral_angle_4_deg	22.021
r_lrange_it	5.399
r_lrange_other	5.399
r_dihedral_angle_1_deg	3.803
r_mcangle_it	3.074
r_mcangle_other	3.074
r_scangle_it	2.504
r_scangle_other	2.504
r_mcbond_it	1.973
r_mcbond_other	1.972
r_scbond_it	1.66
r_scbond_other	1.66
r_angle_other_deg	1.414
r_angle_refined_deg	1.094
r_symmetry_nbd_refined	0.297
r_nbd_other	0.229
r_symmetry_nbd_other	0.204
r_nbd_refined	0.191
r_nbtor_refined	0.171
r_symmetry_nbtor_other	0.076
r_xyhbond_nbd_refined	0.068
r_chiral_restr	0.044
r_chiral_restr_other	0.021
r_symmetry_xyhbond_nbd_refined	0.019
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14004
Nucleic Acid Atoms
Solvent Atoms	734
Heterogen Atoms	423

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing