6ZQ0

Structure of a-l-AraAZI-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZPS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	10 mg/mL MgGH51 in 10 mM NaOAc, pH 5.5, 100 mM NaCl mixed 2:1 with 20% PEG 3350, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M NaNO3

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.05	α = 90
b = 65.46	β = 90
c = 191.82	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 PILATUS 6M-F		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.54	61.95	99.7	0.043	0.999	10.6	7.7		110936			18.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.57	99.7		0.731	0.505	0.9	6.4

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	6ZPS	1.54	61.95	110838	5515	99.942	0.18	0.1786	0.2058	19.586

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]
1.685			-2.031		0.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.883
r_dihedral_angle_4_deg	16.806
r_dihedral_angle_3_deg	11.226
r_dihedral_angle_1_deg	7.548
r_lrange_it	3.998
r_lrange_other	3.812
r_scangle_it	2.978
r_scangle_other	2.978
r_scbond_it	2.126
r_scbond_other	2.126
r_mcangle_it	1.892
r_mcangle_other	1.892
r_angle_refined_deg	1.756
r_angle_other_deg	1.528
r_mcbond_it	1.416
r_mcbond_other	1.416
r_symmetry_xyhbond_nbd_refined	0.262
r_nbd_refined	0.204
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.179
r_nbd_other	0.139
r_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.11
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4760
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	134

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing