8BAX | pdb_00008bax

X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - azotochelin complex.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Morph C8: 12.5% PEG1K; 12.5% PEG 3350; 12.5% MPD; 0.03M each NPS (NaNO3, Na2HPO4, (NH4)2SO4); 0.1M MOPS/HEPES pH7.5. Ligand: 1.67mM Fe azotochelin-sulf/pyr-Ir catalyst, 1:1 protein:ligand ratio.

Crystal Properties
Matthews coefficient	Solvent content
2	38.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.158	α = 90
b = 66.652	β = 90
c = 117.055	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 EIGER2 S 16M		2022-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	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	1.38	58.596	97.5	0.128	0.138	0.051	0.998	8.2	13.6		54541

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	1.38	1.4			4.439	4.775	1.752	0.473		14.2

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	FREE R-VALUE	8BPX	1.38	58.596	54461	2753	97.353	0.217	0.2141	0.22	0.2622	0.26	30.655

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]
-3.51			-4.427		7.937

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	22.582
r_dihedral_angle_6_deg	15.601
r_dihedral_angle_3_deg	14.992
r_lrange_other	7.391
r_lrange_it	7.386
r_scangle_it	7.301
r_scangle_other	7.299
r_mcangle_other	6.837
r_mcangle_it	6.834
r_scbond_other	6.831
r_scbond_it	6.828
r_dihedral_angle_1_deg	6.54
r_mcbond_it	5.826
r_mcbond_other	5.805
r_dihedral_angle_2_deg	3.345
r_angle_refined_deg	1.395
r_angle_other_deg	0.513
r_nbd_refined	0.231
r_nbd_other	0.222
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.177
r_symmetry_nbd_refined	0.132
r_xyhbond_nbd_other	0.083
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2214
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	31

Software

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