8IP1

Escherichia coli OpgD mutant-D388N with beta-1,2-glucan

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	MMT (pH 4.0), PEG1500, Beta-1,2-glucan

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.092	α = 90
b = 87.099	β = 101.132
c = 110.853	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 S 6M		2022-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	2.06	47.74	99.3	0.996	12.8	6.5		66585

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	2.06	2.11			0.697

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.06	47.74	66562	3252	99.212	0.178	0.1751	0.224	22.845

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]
-1.061		-1.133	2.574		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.79
r_dihedral_angle_4_deg	19.37
r_dihedral_angle_3_deg	13.956
r_dihedral_angle_1_deg	7.466
r_lrange_other	4.337
r_lrange_it	4.321
r_scangle_it	3.159
r_scangle_other	3.159
r_angle_other_deg	3.138
r_mcangle_it	2.192
r_mcangle_other	2.192
r_scbond_it	2.024
r_scbond_other	2.024
r_angle_refined_deg	1.597
r_mcbond_it	1.493
r_mcbond_other	1.491
r_nbd_other	0.264
r_symmetry_nbd_other	0.216
r_nbd_refined	0.198
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.127
r_symmetry_nbd_refined	0.11
r_symmetry_xyhbond_nbd_other	0.095
r_chiral_restr	0.073
r_bond_other_d	0.034
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8157
Nucleic Acid Atoms
Solvent Atoms	566
Heterogen Atoms	290

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing