7YL6 | pdb_00007yl6

Cell surface protein YwfG protein complexed with alpha-1,2-mannobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7YL4

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
4.37	71.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.454	α = 90
b = 276.634	β = 90
c = 321.75	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		2020-12-11	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	2.95	43.06	99.9	0.203	0.211	0.058	0.996	14	13		42029

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	2.95	3.11			1.187	1.232	0.329	0.774	2.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	7YL4	2.95	41.511	42023	2151	99.888	0.214	0.2114	0.22	0.2684	0.27	65.208

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]
-1.638			1.913		-0.276

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.927
r_dihedral_angle_3_deg	21.631
r_dihedral_angle_4_deg	18.724
r_lrange_it	13.987
r_lrange_other	13.962
r_scangle_it	12.238
r_scangle_other	12.046
r_mcangle_it	10.738
r_mcangle_other	10.738
r_scbond_it	8.476
r_scbond_other	8.322
r_mcbond_it	7.546
r_mcbond_other	7.539
r_dihedral_angle_1_deg	6.875
r_angle_refined_deg	2.033
r_angle_other_deg	1.406
r_metal_ion_refined	0.358
r_nbd_refined	0.212
r_nbd_other	0.21
r_symmetry_nbd_other	0.209
r_symmetry_nbd_refined	0.196
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_refined	0.045
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6534
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	98

Software

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