6S82 | pdb_00006s82

Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Tris-buffer molecule And hydroquinone

X-RAY DIFFRACTION

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	1.3 M Sodium Citrate tribasic dihydrate, 0.1M TRIS-HCl pH 8.5, then soaked in hidroquinone

Crystal Properties
Matthews coefficient	Solvent content
4.12	70.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.579	α = 90
b = 205.623	β = 90
c = 145.369	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	2016-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979490	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.85	83.94	100	0.079	0.032	14.5	6.8		190741

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88			0.559	0.227	2.9

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	1.85	83.94	181015	9619	99.92	0.1552	0.1541	0.17	0.1753	0.18	RANDOM	26.471

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]
0.97			-2.66		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.939
r_dihedral_angle_4_deg	18.018
r_dihedral_angle_3_deg	11.136
r_dihedral_angle_1_deg	7.574
r_angle_refined_deg	1.755
r_angle_other_deg	1.482
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.939
r_dihedral_angle_4_deg	18.018
r_dihedral_angle_3_deg	11.136
r_dihedral_angle_1_deg	7.574
r_angle_refined_deg	1.755
r_angle_other_deg	1.482
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9588
Nucleic Acid Atoms
Solvent Atoms	1348
Heterogen Atoms	953

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.