7KR6

Glycoside hydrolase family 16 endo-glucanase from Bacteroides ovatus in complex with G4G3G-2F-DNP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		278	0.2 M sodium chloride, 0.1 M Tris pH 8.5, 25% (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.447	α = 90
b = 84.576	β = 93.983
c = 67.105	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	100	PIXEL	DECTRIS PILATUS3 S 6M		2020-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979	SSRL	BL12-2

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	1.56	39.4	98.7	1	14.2	2		143215

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	1.56	1.59			0.935

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5NBO	1.56	39.4	72529	3598	98.568	0.173	0.1722	0.18	0.1985	0.21	24.81

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]
0.829		-2.23	0.966		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.116
r_dihedral_angle_4_deg	17.786
r_dihedral_angle_3_deg	12.465
r_dihedral_angle_1_deg	8.235
r_lrange_it	5.332
r_lrange_other	5.265
r_scangle_it	4.46
r_scangle_other	4.46
r_scbond_it	2.991
r_scbond_other	2.991
r_mcangle_other	2.926
r_mcangle_it	2.919
r_angle_other_deg	2.704
r_mcbond_it	2.177
r_mcbond_other	2.161
r_angle_refined_deg	1.707
r_symmetry_nbd_other	0.213
r_nbd_refined	0.183
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.16
r_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.116
r_nbd_other	0.116
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.082
r_bond_other_d	0.036
r_gen_planes_other	0.018
r_bond_refined_d	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3737
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
PHASER	phasing