6ZPX

Structure of Unliganded 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	56.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.98	α = 90
b = 65.801	β = 90
c = 193.12	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		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	1.3	82.28	100	0.035	0.998	6.9	7.8		188207

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	1.3	1.32	99.7		0.422	0.778		6

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	1.3	62.362	188071	9384	99.86	0.18	0.1781	0.2174	18.808

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]
3.335			-1.622		-1.713

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.442
r_dihedral_angle_4_deg	16.759
r_dihedral_angle_3_deg	12.423
r_dihedral_angle_1_deg	7.365
r_rigid_bond_restr	3.843
r_scangle_other	2.801
r_scangle_it	2.797
r_lrange_it	2.673
r_scbond_it	2.622
r_scbond_other	2.622
r_lrange_other	2.552
r_mcangle_other	2.084
r_mcangle_it	2.077
r_angle_refined_deg	1.899
r_mcbond_it	1.834
r_mcbond_other	1.818
r_angle_other_deg	1.593
r_nbd_refined	0.202
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.156
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.118
r_nbd_other	0.114
r_symmetry_xyhbond_nbd_other	0.095
r_symmetry_nbtor_other	0.087
r_symmetry_nbd_refined	0.049
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4769
Nucleic Acid Atoms
Solvent Atoms	643
Heterogen Atoms	124

Software

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