8HCJ

Structure of GH43 family enzyme, Xylan 1, 4 Beta- xylosidase from pseudopedobacter saltans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	18% PEG 3350, 5% PROPANOL, 0.15M IMIDAZOLE

Crystal Properties
Matthews coefficient	Solvent content
2.14	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.34	α = 102.734
b = 89.662	β = 93.985
c = 138.437	γ = 98.237

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	273	PIXEL	DECTRIS PILATUS3 2M		2022-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.96546	ESRF	BM30A

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	2.5	134.29	95	0.08	0.1	0.07	0.94	0.04	1.92		103346			30.2

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)
1	2.5	2.56	97		0.02	0.28	0.19	0.93		2.01

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4NOV	2.566	134.29	103343	5180	95.375	0.166	0.1634	0.2091	33.093

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]
2.558	1.763	0.582	-0.804	0.843	-2.466

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.327
r_dihedral_angle_6_deg	17.669
r_lrange_it	10.506
r_scangle_it	7.745
r_dihedral_angle_1_deg	6.808
r_mcangle_it	6.384
r_scbond_it	5.791
r_dihedral_angle_2_deg	4.871
r_mcbond_it	4.519
r_angle_refined_deg	1.494
r_nbtor_refined	0.319
r_nbd_refined	0.206
r_symmetry_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.187
r_metal_ion_refined	0.181
r_xyhbond_nbd_refined	0.164
r_ncsr_local_group_18	0.126
r_ncsr_local_group_23	0.126
r_ncsr_local_group_27	0.125
r_ncsr_local_group_13	0.124
r_ncsr_local_group_14	0.124
r_ncsr_local_group_20	0.124
r_ncsr_local_group_22	0.124
r_ncsr_local_group_25	0.124
r_ncsr_local_group_6	0.123
r_ncsr_local_group_9	0.123
r_ncsr_local_group_19	0.123
r_ncsr_local_group_21	0.123
r_ncsr_local_group_26	0.123
r_ncsr_local_group_28	0.123
r_ncsr_local_group_11	0.122
r_ncsr_local_group_3	0.121
r_ncsr_local_group_4	0.121
r_ncsr_local_group_5	0.121
r_ncsr_local_group_2	0.12
r_ncsr_local_group_7	0.12
r_ncsr_local_group_16	0.12
r_ncsr_local_group_1	0.118
r_ncsr_local_group_10	0.118
r_ncsr_local_group_12	0.118
r_ncsr_local_group_24	0.118
r_ncsr_local_group_15	0.115
r_ncsr_local_group_17	0.113
r_ncsr_local_group_8	0.111
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27430
Nucleic Acid Atoms
Solvent Atoms	1325
Heterogen Atoms	16

Software

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