9TDV | pdb_00009tdv

Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with raffinose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	0.1M Bis-Tris, pH 5.5 and 2M ammonium sulfate using 2:1 ratio (protein:reservoir). Cryoprotected with 20% glycerol and flash-cooled in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.145	α = 90
b = 141.075	β = 90
c = 252.71	γ = 90

Symmetry
Space Group	P 21 21 21

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		2025-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	48.654	100	0.171	0.069	0.999	16.3	13.5		191260

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.02	100		0.531	0.704	2.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	2	48.654	191149	9648	99.986	0.176	0.1746	0.1829	0.1953	0.2039	29.472

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]
1.133			-0.403		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.028
r_dihedral_angle_2_deg	12.174
r_dihedral_angle_3_deg	11.206
r_dihedral_angle_1_deg	7.267
r_lrange_other	6.59
r_lrange_it	6.586
r_scangle_it	5.049
r_scangle_other	5.049
r_mcangle_it	3.856
r_mcangle_other	3.856
r_scbond_it	3.395
r_scbond_other	3.395
r_mcbond_it	2.709
r_mcbond_other	2.708
r_angle_refined_deg	1.427
r_angle_other_deg	0.802
r_nbd_other	0.33
r_symmetry_nbd_refined	0.295
r_symmetry_nbd_other	0.217
r_nbd_refined	0.216
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_other	0.133
r_symmetry_nbtor_other	0.126
r_chiral_restr	0.076
r_ncsr_local_group_1	0.062
r_ncsr_local_group_2	0.061
r_ncsr_local_group_3	0.059
r_ncsr_local_group_6	0.058
r_ncsr_local_group_4	0.057
r_ncsr_local_group_5	0.056
r_bond_other_d	0.016
r_gen_planes_other	0.011
r_gen_planes_refined	0.01
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16604
Nucleic Acid Atoms
Solvent Atoms	1104
Heterogen Atoms	785

Software

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