6M0E | pdb_00006m0e

Beijerinckia indica beta-fructosyltransferase complexed with fructose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M0D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	30% (w/v) polyethylene glycol 10000, 0.2 M MgCl2, 0.1 M Na K tartrate, 0.1 M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.377	α = 90
b = 81.521	β = 90
c = 99.081	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 EIGER X 16M		2018-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	1.35	45.2	98.9	0.047	0.02	19.4	6.6		96105

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	1.35	1.42	97.7		0.468	0.19	4.1	6.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6M0D	1.35	45.2	96024	4663	98.683	0.151	0.1499	0.15	0.1663	0.17	15.306

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]
			-0.001		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.462
r_dihedral_angle_4_deg	14.977
r_dihedral_angle_3_deg	11.648
r_dihedral_angle_1_deg	7.272
r_lrange_it	4.316
r_lrange_other	3.981
r_scangle_it	2.345
r_scangle_other	2.345
r_angle_other_deg	2.31
r_mcangle_other	1.738
r_mcangle_it	1.735
r_scbond_it	1.499
r_scbond_other	1.498
r_angle_refined_deg	1.47
r_mcbond_it	1.082
r_mcbond_other	1.067
r_nbd_other	0.232
r_symmetry_nbd_other	0.207
r_nbd_refined	0.196
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.071
r_symmetry_nbd_refined	0.063
r_bond_other_d	0.036
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3701
Nucleic Acid Atoms
Solvent Atoms	583
Heterogen Atoms	63

Software

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