9H6G | pdb_00009h6g

Inactive Bacteroides ovatus GH98 endoxylanase E361A in complex with arabino-xylooligosaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		UNRELEASED SAD MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	Vapour diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.05	α = 90
b = 63.485	β = 118.443
c = 180.9	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 6M		2022-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.89842	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.8	53.02	99.9	0.22	0.259	0.136	0.982	6.2	6.9		46262

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.9	99.8		1.143	1.341	0.698	0.63	1.5	7

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	2.8	53.02	46243	2395	99.829	0.19	0.1859	0.1851	0.268	0.2701	45.555

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]
0.547		-1.082	0.96		-0.212

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.968
r_dihedral_angle_6_deg	14.455
r_dihedral_angle_2_deg	10.227
r_dihedral_angle_1_deg	8.376
r_lrange_it	6.566
r_lrange_other	6.561
r_scangle_it	4.422
r_scangle_other	4.422
r_mcangle_it	4.34
r_mcangle_other	4.34
r_scbond_it	2.751
r_scbond_other	2.751
r_mcbond_it	2.656
r_mcbond_other	2.656
r_angle_refined_deg	1.793
r_angle_other_deg	0.611
r_symmetry_xyhbond_nbd_refined	0.319
r_symmetry_nbd_refined	0.248
r_nbd_other	0.219
r_nbd_refined	0.209
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.158
r_metal_ion_refined	0.124
r_symmetry_xyhbond_nbd_other	0.123
r_ncsr_local_group_1	0.091
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14228
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	157

Software

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