8BJ9

X-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - 5LICAM complex.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BF6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Opt 17. E9. 18% PEG 3350, 0.1M TRIS, pH8.5, 0.05M ZnAc, Cryo ethylene glycol. Ligand: 5mM Fe(III) 5-LICAM 1:10 ratio protein:ligand.

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.063	α = 90
b = 117.392	β = 90
c = 141.712	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 EIGER2 S 16M		2022-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976238	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.069	36.83	99.7	0.101	0.105	0.029	0.988	13.3	23.1		18904

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.13			3.363	3.648	1.396	0.238		13

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8BF6	2.069	36.827	18840	938	99.493	0.213	0.2097	0.2656	84.136

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]
3.691			-4.534		0.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.912
r_dihedral_angle_6_deg	14.707
r_dihedral_angle_1_deg	7.099
r_lrange_it	6.825
r_lrange_other	6.825
r_dihedral_angle_2_deg	5.789
r_scangle_it	5.096
r_scangle_other	5.034
r_mcangle_it	4.361
r_mcangle_other	4.359
r_scbond_it	3.636
r_scbond_other	3.456
r_mcbond_it	3.285
r_mcbond_other	3.285
r_angle_refined_deg	1.25
r_symmetry_nbd_refined	0.523
r_angle_other_deg	0.419
r_symmetry_xyhbond_nbd_refined	0.31
r_nbd_refined	0.241
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.165
r_nbd_other	0.122
r_symmetry_metal_ion_refined	0.096
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.059
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2167
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	37

Software

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