6M0D | pdb_00006m0d

Beijerinckia indica beta-fructosyltransferase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W18

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
1.74	29.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.891	α = 90
b = 80.9	β = 90
c = 92.661	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		2019-03-19	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)	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	2.2	46.3	99.8	0.125	0.054	0.992	9.6	6.4		20772

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	2.2	2.23	99.7		0.338	0.14	0.935	4.8

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	1W18	2.2	44.3	20660	1011	99.298	0.224	0.2217	0.23	0.2657	0.27	28.338

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]
-0.006			0.014		-0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.734
r_dihedral_angle_3_deg	15.42
r_dihedral_angle_4_deg	13.269
r_dihedral_angle_1_deg	8.058
r_lrange_it	5.293
r_lrange_other	5.288
r_scangle_it	3.815
r_scangle_other	3.814
r_mcangle_it	3.269
r_mcangle_other	3.269
r_scbond_it	2.601
r_scbond_other	2.601
r_angle_other_deg	2.41
r_mcbond_it	2.233
r_mcbond_other	2.231
r_angle_refined_deg	1.636
r_symmetry_nbd_refined	0.286
r_nbd_other	0.271
r_symmetry_xyhbond_nbd_refined	0.242
r_symmetry_nbd_other	0.217
r_nbd_refined	0.202
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.16
r_metal_ion_refined	0.149
r_symmetry_xyhbond_nbd_other	0.077
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.069
r_bond_other_d	0.036
r_gen_planes_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3694
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	2

Software

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