5Z3B

Glycosidase Y48F

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.2M Ammonium citrate tribasic (pH 6.8), 0.1M Sodium citrate (pH 5.5), 12% PEGmonomethyl ether 2000, 2mM glucose

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.658	α = 90
b = 104.658	β = 90
c = 89.376	γ = 90

Symmetry
Space Group	P 4 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	CCD	ADSC QUANTUM 315		2017-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	1.25	89.38	99.9	28.01	14.3		136595

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	1.25	1.32

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.25	45.16	129766	6829	99.9	0.11205	0.11135	0.12508	RANDOM	16.615

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]
0.17			0.17		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.281
r_sphericity_free	26.518
r_dihedral_angle_4_deg	20.636
r_sphericity_bonded	11.356
r_dihedral_angle_3_deg	10.819
r_rigid_bond_restr	5.763
r_dihedral_angle_1_deg	5.412
r_scangle_other	4.17
r_long_range_B_other	3.855
r_long_range_B_refined	3.854
r_scbond_it	3.595
r_scbond_other	3.578
r_mcangle_it	2.111
r_mcangle_other	2.11
r_angle_refined_deg	1.668
r_mcbond_it	1.63
r_mcbond_other	1.624
r_angle_other_deg	0.896
r_chiral_restr	0.122
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.001
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2861
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing