8JEA

Crystal structure of CGL1 from Crassostrea gigas, mannotriose-bound form (CGL1/Man(alpha)1-2Man(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% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.734	α = 90
b = 58.674	β = 93.657
c = 108.41	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	0.97	39.771	100	0.036	1	28.6	12.8		292966

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	0.97	0.99			1.021	0.82

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	0.97	39.771	292928	14810	99.988	0.176	0.1751	0.1885	11.064

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		-0.001	0.015		-0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.915
r_rigid_bond_restr	15.562
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_1_deg	7.24
r_dihedral_angle_2_deg	4.098
r_lrange_it	3.374
r_lrange_other	3.341
r_scangle_it	2.931
r_scangle_other	2.931
r_scbond_other	2.929
r_scbond_it	2.928
r_mcangle_it	2.221
r_mcangle_other	2.221
r_mcbond_it	2.142
r_mcbond_other	2.142
r_angle_refined_deg	1.799
r_angle_other_deg	0.993
r_symmetry_nbd_refined	0.296
r_nbd_other	0.251
r_symmetry_nbd_other	0.212
r_nbd_refined	0.211
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.107
r_chiral_restr	0.099
r_gen_planes_other	0.022
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4360
Nucleic Acid Atoms
Solvent Atoms	815
Heterogen Atoms	95

Software

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