6F4C

Nicotiana benthamiana alpha-galactosidase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.2 M LiSO4 0.1 M BIS-TRIS 5.5 pH 25 %w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.037	α = 90
b = 74.037	β = 90
c = 133.307	γ = 90

Symmetry
Space Group	P 41 21 2

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 EIGER X 4M	CRL	2016-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.8	64.72	98.8	5.4	7.2		9569

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	64.72

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1uas	2.8	64.72	9060	486	98.59	0.21432	0.21058	0.28505	RANDOM	3.809

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]
0.5			0.5		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.106
r_dihedral_angle_4_deg	18.221
r_dihedral_angle_3_deg	14.858
r_dihedral_angle_1_deg	7.307
r_angle_other_deg	2.102
r_angle_refined_deg	1.545
r_long_range_B_refined	1.223
r_long_range_B_other	1.219
r_mcangle_it	0.36
r_mcangle_other	0.36
r_scangle_other	0.216
r_mcbond_it	0.191
r_mcbond_other	0.19
r_scbond_it	0.109
r_scbond_other	0.109
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2799
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms

Software

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