8P1X | pdb_00008p1x

TarM(Se)_G117R-UDP-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, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.65	α = 90
b = 88.73	β = 90
c = 98.05	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 2M		2020-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00000	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	2.03	49.03	100	0.999	15.64	13.2		33765

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	2.03	2.08	100		0.52

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	2.03	49.025	33764	1689	99.976	0.203	0.2012	0.21	0.2381	0.24	34.271

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]
4.034			-0.139		-3.895

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.614
r_dihedral_angle_4_deg	17.389
r_dihedral_angle_3_deg	15.39
r_lrange_it	8.052
r_lrange_other	8.052
r_scangle_it	6.093
r_scangle_other	6.092
r_mcangle_it	5.632
r_mcangle_other	5.632
r_dihedral_angle_1_deg	5.562
r_scbond_it	4.948
r_scbond_other	4.947
r_mcbond_it	4.674
r_mcbond_other	4.654
r_angle_other_deg	1.341
r_angle_refined_deg	1.143
r_symmetry_nbd_refined	0.233
r_symmetry_nbd_other	0.181
r_nbd_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.178
r_nbd_other	0.168
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.058
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3847
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	81

Software

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