8BAW

X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - 5-LICAM siderophore analogue 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		293	Morpheus A12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03M of each divalent cation (MgCl2, CaCl2), 0.1M Bicine/Trizma base pH 8.5 5mM Fe(III) 5-LICAM 1:10 ratio protein:ligand. No cryo.

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.395	α = 90
b = 34.432	β = 92.889
c = 119.109	γ = 90

Symmetry
Space Group	P 1 21 1

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		2020-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.93622	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	1.47	67.4	99.8	0.04	0.048	0.026	0.999	14.6	6.5		93663

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	1.47	1.5			2.86	3.423	1.86	0.432		6.3

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	1.471	67.4	93643	4698	99.791	0.182	0.1797	0.2326	42.224

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]
2.02		-1.192	-1.941		0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.302
r_dihedral_angle_6_deg	15.281
r_lrange_other	9.142
r_lrange_it	9.141
r_scangle_it	9.136
r_scangle_other	9.135
r_rigid_bond_restr	8.281
r_scbond_it	8.127
r_scbond_other	8.125
r_mcangle_it	8.012
r_mcangle_other	8.012
r_mcbond_it	7.861
r_mcbond_other	7.852
r_dihedral_angle_1_deg	6.326
r_dihedral_angle_2_deg	3.784
r_angle_refined_deg	1.345
r_angle_other_deg	0.464
r_symmetry_nbd_refined	0.243
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_refined	0.215
r_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.189
r_nbd_other	0.181
r_nbtor_refined	0.178
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.053
r_xyhbond_nbd_other	0.051
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4357
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	56

Software

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