8BF6

X-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - azotochelin complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	25% PEG 1500; 0.1 M PCMB pH 4.0 (Na propionate: Na cacodylate: BisTris propane 2:1:2). LIgand: 5mM Fe(III) Azotochelin (Washed) 1:10 ratio protein:ligand.

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.295	α = 90
b = 116.711	β = 90
c = 141.471	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		2020-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.979499	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	1.969	70.836	100	0.069	0.074	0.028	1	16.4	12.8		21889

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	1.97	2.02			2.703	2.922	1.1	0.408		13.3

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	8PBX	1.969	70.836	21853	1084	99.963	0.207	0.2048	0.2547	59.941

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]
0.03			-0.871		0.841

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.939
r_dihedral_angle_6_deg	16.504
r_dihedral_angle_2_deg	7.528
r_dihedral_angle_1_deg	7.095
r_lrange_it	6.146
r_lrange_other	6.14
r_scangle_other	4.979
r_scangle_it	4.976
r_scbond_it	3.511
r_scbond_other	3.506
r_mcangle_it	3.315
r_mcangle_other	3.314
r_mcbond_it	2.538
r_mcbond_other	2.538
r_angle_refined_deg	1.348
r_angle_other_deg	0.55
r_symmetry_nbd_refined	0.429
r_symmetry_xyhbond_nbd_refined	0.332
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.222
r_symmetry_nbd_other	0.191
r_nbd_other	0.181
r_nbtor_refined	0.179
r_symmetry_nbtor_other	0.08
r_symmetry_metal_ion_refined	0.063
r_chiral_restr	0.058
r_bond_other_d	0.015
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
r_metal_ion_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2167
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	41

Software

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