6TVK | pdb_00006tvk

Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	283.15	Condition: 0.1 M NaCl, 1.5 M ammonium acetate, 0.1 M BIS-TRIS pH 6.5 The condition was diluted to 80% 5 mM maltose as an additive

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.118	α = 90
b = 125.118	β = 90
c = 231.905	γ = 120

Symmetry
Space Group	P 64 2 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 PILATUS 2M		2019-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.1	49.08	99.7	0.141	0.144	0.031	1	25.5	40.1		63022			43.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	100		3.57	3.653	0.77	0.822	1.9	42.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.1	49.08	59829		99.617	0.189	0.1887	0.1962	0.2252	0.2052	52.086

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]
1.83	0.915		1.83		-5.937

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.627
r_dihedral_angle_4_deg	17.521
r_dihedral_angle_3_deg	14.166
r_lrange_it	7.28
r_lrange_other	7.279
r_dihedral_angle_1_deg	7.272
r_scangle_it	6.354
r_scangle_other	6.323
r_scbond_it	4.71
r_scbond_other	4.667
r_mcangle_it	4.429
r_mcangle_other	4.428
r_mcbond_it	3.579
r_mcbond_other	3.578
r_angle_refined_deg	1.553
r_angle_other_deg	1.32
r_nbd_other	0.216
r_symmetry_nbd_refined	0.214
r_nbd_refined	0.194
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.116
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.059
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5231
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	42

Software

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