22HK | pdb_000022hk

Beta-1,2-glucan-binding protein complexed with cyclc beta-1,2-glucononadecaose

X-RAY DIFFRACTION

---

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-glucononadecaose

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.488	α = 90
b = 83.197	β = 90
c = 94.235	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	1.27	47.28	100	1	35.6	12.8		150304

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	1.27	1.29	100		0.907

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	1.27	47.278	150194	7517	99.977	0.166	0.1652	0.1746	0.1807	0.1882	16.812

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]
0.012			-0.002		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.969
r_dihedral_angle_3_deg	12.717
r_dihedral_angle_2_deg	11.91
r_dihedral_angle_1_deg	6.211
r_lrange_it	4.798
r_lrange_other	4.732
r_scangle_it	4.236
r_scangle_other	4.21
r_scbond_it	2.894
r_scbond_other	2.879
r_mcangle_other	2.173
r_mcangle_it	2.169
r_angle_refined_deg	1.92
r_mcbond_it	1.559
r_mcbond_other	1.559
r_angle_other_deg	1.028
r_nbd_refined	0.399
r_nbd_other	0.251
r_symmetry_nbd_refined	0.245
r_symmetry_nbd_other	0.213
r_symmetry_xyhbond_nbd_refined	0.202
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_other	0.132
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_other	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3376
Nucleic Acid Atoms
Solvent Atoms	412
Heterogen Atoms	237

Software

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