7YL5

Cell surface protein YwfG protein complexed with mannose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M sodium acetate (pH 5.0-5.6), 1.3 M Li2SO4, 2% (w/v) polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
4.42	72.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.312	α = 90
b = 273.164	β = 90
c = 322.789	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS3 S 2M		2019-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3	48.71	100	0.145	0.151	0.042	0.998	16	6.8		39549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.16	100		1.053	1.097	0.304	0.806	2.7	6.7

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	FOURIER SYNTHESIS	FREE R-VALUE	7YL4	3	45.569	39421	1964	99.628	0.23	0.2271	0.2955	79.915

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]
0.021			-0.086		0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.434
r_dihedral_angle_4_deg	22.122
r_dihedral_angle_3_deg	21.523
r_lrange_other	18.644
r_lrange_it	18.63
r_scangle_it	16.882
r_scangle_other	16.286
r_mcangle_it	15.25
r_mcangle_other	15.25
r_scbond_it	12.625
r_scbond_other	11.972
r_mcbond_it	11.491
r_mcbond_other	11.484
r_dihedral_angle_1_deg	7.695
r_angle_refined_deg	2.279
r_angle_other_deg	1.437
r_metal_ion_refined	0.385
r_nbd_other	0.26
r_symmetry_xyhbond_nbd_refined	0.242
r_nbd_refined	0.22
r_symmetry_nbd_other	0.213
r_nbtor_refined	0.188
r_symmetry_nbd_refined	0.182
r_xyhbond_nbd_refined	0.167
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.088
r_symmetry_xyhbond_nbd_other	0.087
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6446
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	163

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing