22HJ | pdb_000022hj

Beta-1,2-glucan-binding protein soaked with cyclic beta-1,2-glucooctaose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	22HH

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.699	α = 90
b = 82.849	β = 90
c = 94.099	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 6M		2023-12-23	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	1.6	47.25	100	1	33.9	12.4		75627

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	1.6	1.63	99.9		0.946

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	1.6	35.992	75525	3838	99.938	0.168	0.1668	0.1796	0.1813	0.1924	20.339

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]
0.014			-0.005		-0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.037
r_dihedral_angle_2_deg	15.064
r_dihedral_angle_3_deg	12.756
r_dihedral_angle_1_deg	6.156
r_lrange_it	5.655
r_lrange_other	5.655
r_scangle_it	5.259
r_scangle_other	5.169
r_scbond_it	3.586
r_scbond_other	3.535
r_mcangle_other	2.627
r_mcangle_it	2.622
r_mcbond_it	1.981
r_mcbond_other	1.981
r_angle_refined_deg	1.912
r_angle_other_deg	1.042
r_nbd_refined	0.325
r_symmetry_nbd_other	0.214
r_nbd_other	0.214
r_symmetry_nbd_refined	0.2
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.144
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.084
r_gen_planes_other	0.019
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_symmetry_xyhbond_nbd_other	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3375
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	163

Software

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