6ZPW

Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 2

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		293	10 mg/mL MgGH51 in 10 mM NaOAc pH 5.5, 100 mM NaCl mixed 2:1 with 2.4 M (NH4)2SO4, 0.1 M NaOAc, pH 6, 20% glycerol

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.953	α = 90
b = 125.838	β = 90
c = 161.226	γ = 90

Symmetry
Space Group	C 2 2 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		2019-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.329	80.743	99.9	0.035	0.999	9.6	8		265496

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	1.33	1.35	98		0.727	0.521	1.1	6.8

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	FREE R-VALUE	6ZPS	1.329	80.743	265473	13118	99.849	0.131	0.1303	0.1511	15.393

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]
-0.249			-0.341		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.039
r_dihedral_angle_4_deg	15.701
r_dihedral_angle_3_deg	11.315
r_dihedral_angle_1_deg	7.043
r_rigid_bond_restr	3.555
r_scangle_it	3.111
r_scangle_other	3.111
r_lrange_it	3.027
r_lrange_other	2.775
r_scbond_it	2.614
r_scbond_other	2.614
r_angle_refined_deg	1.931
r_mcangle_it	1.724
r_mcangle_other	1.724
r_angle_other_deg	1.655
r_mcbond_it	1.569
r_mcbond_other	1.505
r_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.178
r_nbd_other	0.167
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.116
r_symmetry_nbd_refined	0.107
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4788
Nucleic Acid Atoms
Solvent Atoms	719
Heterogen Atoms	229

Software

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