5FMD

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with nystose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		PROTEIN WAS CRYSTALLIZED FROM 1.25M SODIUM CITRATE TRIBASIC DIHYDRATE, THEN SOAKED IN 50MM NYSTOSE, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.08	70.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.552	α = 90
b = 205.405	β = 90
c = 146.362	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	2014-07-16	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.78	119.2	100	0.07	16.2	6.7		215107

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	100		0.55	3.6	6.7

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	PDB ENTRY 5ANN	1.78	119.2	204249	10741	99.97	0.16717	0.16661	0.17782	RANDOM	25.93

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]
1.32			-2.22		0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.247
r_dihedral_angle_4_deg	16.818
r_dihedral_angle_3_deg	10.231
r_dihedral_angle_1_deg	6.662
r_scbond_it	1.756
r_mcangle_it	1.463
r_angle_refined_deg	1.371
r_angle_other_deg	0.976
r_mcbond_it	0.931
r_mcbond_other	0.931
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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	1444
Heterogen Atoms	911

Software

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