8B73 | pdb_00008b73

Acetivibrio clariflavus beta-1,4-xylanase of Glycoside Hydrolase Family 10 (AcXyn10A).

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.4	293.15	H6 conditions of JCSG+ HTS 0.1 M Ammonium acetate 0.1 M BIS-Tris, 17 % w/v PEG 10,000 109.79mM Xyltetraose (10X) with AcXynA protein in buffer containing 50mM NaCl, 20mM Tris-Cl

Crystal Properties
Matthews coefficient	Solvent content
3.27243114	62.436615

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.566	α = 90
b = 88.916	β = 90
c = 173.479	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 XE 16M		2021-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9793	Diamond	I03

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	2.24	89.58	99.81	0.166	0.173	0.05	0.997	8	12.7		61326			46.76

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.24	2.29	100		2.685	0.764	0.405		13.5

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	SAD	FREE R-VALUE	2.24	62.089	60339	3049	99.376	0.207	0.206	0.22	0.2316	0.24	52.222

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]
-0.412			-0.407		0.819

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.934
r_dihedral_angle_6_deg	13.832
r_dihedral_angle_1_deg	6.278
r_dihedral_angle_2_deg	5.448
r_lrange_it	2.386
r_lrange_other	2.38
r_scangle_it	1.196
r_scangle_other	1.195
r_mcangle_it	1.174
r_mcangle_other	1.174
r_angle_refined_deg	0.95
r_scbond_it	0.706
r_scbond_other	0.706
r_mcbond_it	0.674
r_mcbond_other	0.674
r_angle_other_deg	0.341
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_other	0.209
r_symmetry_nbd_refined	0.196
r_nbd_refined	0.192
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.156
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.049
r_ncsr_local_group_1	0.04
r_symmetry_xyhbond_nbd_other	0.005
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6578
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2.multiplex	data scaling
PHASER	phasing