7XSH

Crystal structure of ClAgl29B bound with L-glucose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7XSG	Apo form

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	0.1 M sodium citrate (pH 3.5), 5% PEG 20,000, 5% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.393	α = 90
b = 121.583	β = 90
c = 166.372	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		2021-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	1.708	98.164	99.8	0.093	0.101	0.999	17.44	6.7		159024			27.15

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.81	99.1		0.863	0.942	0.81	2.37	6.2

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	MOLECULAR REPLACEMENT	FREE R-VALUE	Apo form	1.708	46.598	159021	7948	99.827	0.18	0.1789	0.2016	24.522

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]
0.261			1.425		-1.686

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.146
r_dihedral_angle_3_deg	14.408
r_dihedral_angle_2_deg	13.178
r_dihedral_angle_1_deg	6.564
r_lrange_it	5.579
r_lrange_other	5.491
r_scangle_it	4.086
r_scangle_other	4.086
r_mcangle_it	3.083
r_mcangle_other	3.083
r_scbond_it	2.655
r_scbond_other	2.654
r_mcbond_it	2.076
r_mcbond_other	2.075
r_angle_refined_deg	1.287
r_angle_other_deg	0.453
r_symmetry_nbd_refined	0.276
r_nbd_other	0.219
r_nbd_refined	0.212
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.172
r_xyhbond_nbd_refined	0.125
r_metal_ion_refined	0.119
r_ncsr_local_group_1	0.09
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8872
Nucleic Acid Atoms
Solvent Atoms	692
Heterogen Atoms	76

Software

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