8JE9

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

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% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.749	α = 90
b = 58.701	β = 93.701
c = 108.405	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	90	PIXEL	DECTRIS PILATUS3 S 6M		2021-12-02	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	39.8	85.9	0.056	0.999	18.6	6.8		229413

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	1.02			0.872

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	39.778	229386	11557	85.767	0.175	0.1744	0.1869	10.872

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]
-0.001		0.013	0.007		-0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.984
r_rigid_bond_restr	14.956
r_dihedral_angle_3_deg	12.517
r_dihedral_angle_1_deg	7.312
r_dihedral_angle_2_deg	4.519
r_lrange_it	2.767
r_lrange_other	2.767
r_angle_refined_deg	1.768
r_scangle_it	1.615
r_scangle_other	1.615
r_mcangle_it	1.466
r_mcangle_other	1.466
r_scbond_other	1.233
r_scbond_it	1.231
r_mcbond_it	1.095
r_mcbond_other	1.095
r_angle_other_deg	1.017
r_symmetry_nbd_refined	0.363
r_nbd_other	0.284
r_symmetry_nbd_other	0.209
r_nbd_refined	0.205
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.118
r_chiral_restr	0.107
r_symmetry_nbtor_other	0.106
r_gen_planes_other	0.016
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4360
Nucleic Acid Atoms
Solvent Atoms	802
Heterogen Atoms	75

Software

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