6SXV

GH51 a-l-arabinofuranosidase soaked with aziridine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PZ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	2:1 protein:well solution. 0.1 M pH 7.5 Tris-HCl buffer, 18% PEG3350, 0.7 M NH4F, 5% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.994	α = 90
b = 178.994	β = 90
c = 100.893	γ = 120

Symmetry
Space Group	H 3

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 16M		2018-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.987	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	29.85	99.5	0.077	0.997	10.8	6.2		235421

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.44	94.5		0.613	0.78	1.5	5.8

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	THROUGHOUT	1PZ3	1.402	29.85	235420	12425	99.512	0.171	0.1702	0.1784	19.467

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]
0.055	0.027		0.055		-0.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.913
r_dihedral_angle_4_deg	19.719
r_dihedral_angle_3_deg	11.714
r_dihedral_angle_1_deg	7.527
r_lrange_it	5.435
r_lrange_other	5.261
r_scangle_it	4.808
r_scangle_other	4.808
r_scbond_it	3.771
r_scbond_other	3.771
r_mcangle_other	2.999
r_mcangle_it	2.997
r_angle_other_deg	2.537
r_mcbond_it	2.464
r_mcbond_other	2.463
r_angle_refined_deg	2.169
r_symmetry_nbd_refined	0.344
r_nbd_other	0.318
r_nbd_refined	0.226
r_symmetry_nbd_other	0.215
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_other	0.145
r_chiral_restr	0.128
r_symmetry_nbtor_other	0.078
r_bond_other_d	0.035
r_gen_planes_other	0.026
r_bond_refined_d	0.019
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7747
Nucleic Acid Atoms
Solvent Atoms	859
Heterogen Atoms	110

Software

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