Experiment: 8XZZ

Structure of a xylanase Xyl-1 M4 E175A in complex with xylobiose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WP4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		295	0.2 M sodium formate, 0.1 M Bis-Tris propane, pH 6.5, and 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.074	α = 90
b = 137.54	β = 97.83
c = 52.848	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 EIGER2 X 9M		2023-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.99987	NSRRC	TPS 05A

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	1.72	24.27	95.5	0.051	0.06	0.031	0.997	21.3	3.9		73843

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.78	90.6		0.152	13.45	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3WP4	1.72	24.27	1.43	73804	2006	95.11	0.1617	0.1608	0.1616	0.1917	0.1927	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.387
f_angle_d	0.897
f_chiral_restr	0.06
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5903
Nucleic Acid Atoms
Solvent Atoms	740
Heterogen Atoms	82

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
DENZO	data reduction
REFMAC	phasing