8POF | pdb_00008pof

The crystal structure of RsSymEG1 reveals a unique form of smaller GH7 endoglucanases alongside GH7 cellobiohydrolases in protist symbionts of termites

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ITasser

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.03 M Sodium fluoride, 0.03 M Sodium bromide, 0.03 M Sodium iodide, 12% v/v PEG 500 MME, 6 % w/v PEG 20000, 0.1 M Tris-Bicine pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.604	α = 90
b = 114.604	β = 90
c = 49.963	γ = 90

Symmetry
Space Group	I 41

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 EIGER X 16M	KB mirrors	2021-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9763	MAX IV	BioMAX

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	1.85	45.8	99.8	0.996	9.8	4.2		27804

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	1.85	1.89			0.821	2.6

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	1.85	45.8	27793	1405	99.731	0.167	0.1659	0.17	0.1866	0.19	20.646

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]
-0.228			-0.228		0.457

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.246
r_dihedral_angle_4_deg	15.06
r_dihedral_angle_3_deg	12.173
r_dihedral_angle_1_deg	7.218
r_lrange_it	3.62
r_lrange_other	3.508
r_angle_other_deg	2.404
r_scangle_it	2.206
r_scangle_other	2.205
r_mcangle_other	1.481
r_mcangle_it	1.48
r_scbond_it	1.37
r_scbond_other	1.37
r_angle_refined_deg	1.226
r_mcbond_it	0.926
r_mcbond_other	0.924
r_symmetry_nbd_other	0.209
r_nbd_refined	0.189
r_nbd_other	0.188
r_symmetry_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.152
r_nbtor_refined	0.149
r_metal_ion_refined	0.127
r_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.067
r_chiral_restr	0.05
r_bond_other_d	0.037
r_symmetry_xyhbond_nbd_other	0.008
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2377
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	9

Software

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