22HH | pdb_000022hh

Beta-1,2-glucan-binding protein complex with linear beta-1,2-glucan

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	ammonium sulfate, bis-Tris, linear beta-1,2-glucan

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.71	α = 90
b = 83.261	β = 90
c = 94.267	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 PILATUS3 6M		2022-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	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	1.53	47.63	100	0.999	18.2	6.5		88131

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	1.53	1.56	100		0.742

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.53	47.628	88053	4385	99.989	0.159	0.1584	0.1723	0.1756	0.1894	18.37

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]
0.009			0.004		-0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.8
r_dihedral_angle_3_deg	12.567
r_dihedral_angle_2_deg	11.566
r_dihedral_angle_1_deg	6.206
r_lrange_it	5.4
r_lrange_other	5.4
r_scangle_it	4.836
r_scangle_other	4.835
r_scbond_it	3.201
r_scbond_other	3.2
r_mcangle_other	2.458
r_mcangle_it	2.457
r_angle_refined_deg	1.821
r_mcbond_it	1.737
r_mcbond_other	1.731
r_angle_other_deg	0.982
r_nbd_refined	0.327
r_nbd_other	0.225
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.19
r_symmetry_nbd_refined	0.189
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.13
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.083
r_gen_planes_other	0.014
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3384
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	169

Software

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