8BAX

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BPX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Morph 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 coefficientSolvent content
238.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.158α = 90
b = 66.652β = 90
c = 117.055γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2022-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97628DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3858.59697.50.1280.1380.0510.9988.213.654541
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)RedundancyNumber Unique Reflections (All)
11.381.44.4394.7751.7520.47314.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE8BPX1.3858.59654461275397.3530.2170.21410.262230.655
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]
-3.51-4.4277.937
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr22.582
r_dihedral_angle_6_deg15.601
r_dihedral_angle_3_deg14.992
r_lrange_other7.391
r_lrange_it7.386
r_scangle_it7.301
r_scangle_other7.299
r_mcangle_other6.837
r_mcangle_it6.834
r_scbond_other6.831
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr22.582
r_dihedral_angle_6_deg15.601
r_dihedral_angle_3_deg14.992
r_lrange_other7.391
r_lrange_it7.386
r_scangle_it7.301
r_scangle_other7.299
r_mcangle_other6.837
r_mcangle_it6.834
r_scbond_other6.831
r_scbond_it6.828
r_dihedral_angle_1_deg6.54
r_mcbond_it5.826
r_mcbond_other5.805
r_dihedral_angle_2_deg3.345
r_angle_refined_deg1.395
r_angle_other_deg0.513
r_nbd_refined0.231
r_nbd_other0.222
r_symmetry_xyhbond_nbd_refined0.215
r_symmetry_nbd_other0.196
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.177
r_symmetry_nbd_refined0.132
r_xyhbond_nbd_other0.083
r_symmetry_nbtor_other0.078
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing