6FJG

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and 4-nitrophenol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ANN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	1.2M Sodium Citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
4.08	73.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.505	α = 90
b = 205.652	β = 90
c = 146.512	γ = 90

Symmetry
Space Group	P 21 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 PILATUS 6M	KB mirrors	2016-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

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	1.73	84.17	100	0.062	0.067	0.026	0.999	16.7	6.8		234346

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5ANN	1.73	119.33	222475	11750	99.95	0.16354	0.16278	0.17	0.17822	0.19	RANDOM	25.413

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]
1.1			-2.11		1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.176
r_dihedral_angle_4_deg	17.976
r_dihedral_angle_3_deg	10.509
r_dihedral_angle_1_deg	6.674
r_long_range_B_refined	5.049
r_long_range_B_other	5.049
r_scangle_other	2.93
r_scbond_it	1.738
r_scbond_other	1.738
r_mcangle_it	1.464
r_mcangle_other	1.464
r_angle_refined_deg	1.443
r_mcbond_it	0.946
r_mcbond_other	0.946
r_angle_other_deg	0.91
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9588
Nucleic Acid Atoms
Solvent Atoms	1546
Heterogen Atoms	955

Software

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