9H6F | pdb_00009h6f

Bacteroides ovatus GH98 endoxylanase 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		From unreleased SAD data

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.05	α = 90
b = 63.85	β = 118.69
c = 180.49	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		2022-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.93932	Diamond	I04

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	2.2	59.18	99.9	0.995	9.3	1.9		94781

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	2.2	2.24	100		0.643	1.4	2

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	2.2	59.176	94779	4758	99.924	0.195	0.1922	0.1922	0.2454	0.2447	40.87

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]
1.257		-1.005	0.671		-0.518

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.574
r_dihedral_angle_3_deg	13.351
r_dihedral_angle_2_deg	10.501
r_dihedral_angle_1_deg	8.007
r_lrange_it	5.334
r_lrange_other	5.319
r_scangle_it	3.397
r_scangle_other	3.397
r_mcangle_it	3.301
r_mcangle_other	3.3
r_scbond_it	2.127
r_scbond_other	2.127
r_mcbond_it	2.015
r_mcbond_other	2.014
r_angle_refined_deg	1.635
r_angle_other_deg	0.56
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.209
r_symmetry_nbd_other	0.192
r_nbd_other	0.19
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.175
r_xyhbond_nbd_refined	0.162
r_metal_ion_refined	0.134
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.077
r_ncsr_local_group_1	0.076
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14243
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	69

Software

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