9TDU | pdb_00009tdu

Structure of Fructofuranosidase from Purpureocilum lilacinum

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	4.6	291	0.1M sodium acetate buffer, pH 4.6 and 2M ammonium sulfate using 2:1 ratio (protein:reservoir). Cryoprotected with 20% PEG400 and flash-cooled in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.412	α = 90
b = 111.693	β = 90
c = 219.254	γ = 90

Symmetry
Space Group	C 2 2 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		2024-07-27	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	2.1	46.9	98.29	0.16	0.068	0.998	14.4	12.2		73064

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	97.05		0.696	0.298	0.939	4.4	11.7

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	46.809	72976	3664	98.372	0.196	0.19573	0.194	0.2025	0.2312	0.2375	RANDOM	20.944

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]
-0.312			0.581		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.165
r_dihedral_angle_6_deg	13.117
r_dihedral_angle_3_deg	11.334
r_dihedral_angle_1_deg	7.163
r_lrange_it	6.178
r_lrange_other	6.167
r_scangle_it	3.991
r_scangle_other	3.991
r_mcangle_it	3.278
r_mcangle_other	3.278
r_scbond_it	2.561
r_scbond_other	2.561
r_mcbond_it	2.057
r_mcbond_other	2.057
r_angle_refined_deg	1.438
r_angle_other_deg	0.768
r_nbd_other	0.27
r_nbd_refined	0.232
r_symmetry_nbd_other	0.222
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.119
r_symmetry_xyhbond_nbd_refined	0.097
r_chiral_restr	0.073
r_ncsr_local_group_1	0.063
r_bond_other_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.01
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8289
Nucleic Acid Atoms
Solvent Atoms	514
Heterogen Atoms	347

Software

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