6ZQ1

Structure of AraDNJ-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
2.82	56.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.803	α = 90
b = 65.914	β = 90
c = 193.563	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 X 16M		2020-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.7	29.87	99.9	0.028	0.999	15.9	34.5		85172			13.5

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	1.7	1.73	99.4		0.281	0.915	2.1	16.3

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	1.7	29.87	85060	4303	99.894	0.196	0.1946	0.2165	19.379

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]
4.511			-1.955		-2.556

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.749
r_dihedral_angle_4_deg	18.266
r_dihedral_angle_3_deg	11.878
r_dihedral_angle_1_deg	7.697
r_lrange_it	4.03
r_lrange_other	3.904
r_scangle_it	2.857
r_scangle_other	2.857
r_mcangle_it	2.057
r_mcangle_other	2.056
r_scbond_it	1.984
r_scbond_other	1.984
r_angle_refined_deg	1.666
r_mcbond_it	1.537
r_mcbond_other	1.536
r_angle_other_deg	1.435
r_symmetry_xyhbond_nbd_refined	0.393
r_nbd_refined	0.196
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.108
r_chiral_restr_other	0.103
r_nbd_other	0.096
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.081
r_bond_refined_d	0.011
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	4767
Nucleic Acid Atoms
Solvent Atoms	545
Heterogen Atoms	133

Software

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