8JEB

Crystal structure of CGL1 from Crassostrea gigas, mannotetraose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man(alpha)1-6Man)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.2 M magnesium acetate, 0.1 M sodium cacodylate (pH 6.5), 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.4	α = 90
b = 82.495	β = 90
c = 44.201	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS PILATUS3 S 6M		2021-11-03	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)	R Merge I (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	1.3	44.201	99.2	0.053	1	22.9	12.5		68918

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32			0.747	0.837

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	1.3	44.201	68858	3467	99.183	0.157	0.1564	0.1745	14.566

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]
-0.002			-0.002		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.681
r_dihedral_angle_3_deg	12.654
r_dihedral_angle_1_deg	7.398
r_lrange_it	4.867
r_lrange_other	4.812
r_scangle_it	4.286
r_scangle_other	4.285
r_dihedral_angle_2_deg	4.192
r_scbond_it	3.005
r_scbond_other	3.004
r_angle_refined_deg	1.655
r_mcangle_it	1.483
r_mcangle_other	1.483
r_mcbond_it	1.092
r_mcbond_other	1.057
r_symmetry_nbd_refined	0.735
r_angle_other_deg	0.579
r_chiral_restr	0.313
r_nbd_refined	0.256
r_symmetry_nbd_other	0.219
r_nbd_other	0.194
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.045
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2180
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	115

Software

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