8BF6

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429325% 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 coefficientSolvent content
2.2946.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.295α = 90
b = 116.711β = 90
c = 141.471γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2020-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.979499DiamondI03

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
11.96970.8361000.0690.0740.028116.412.821889
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)
11.972.022.7032.9221.10.40813.3

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-VALUE8PBX1.96970.83621853108499.9630.2070.20480.254759.941
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]
0.03-0.8710.841
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.939
r_dihedral_angle_6_deg16.504
r_dihedral_angle_2_deg7.528
r_dihedral_angle_1_deg7.095
r_lrange_it6.146
r_lrange_other6.14
r_scangle_other4.979
r_scangle_it4.976
r_scbond_it3.511
r_scbond_other3.506
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.939
r_dihedral_angle_6_deg16.504
r_dihedral_angle_2_deg7.528
r_dihedral_angle_1_deg7.095
r_lrange_it6.146
r_lrange_other6.14
r_scangle_other4.979
r_scangle_it4.976
r_scbond_it3.511
r_scbond_other3.506
r_mcangle_it3.315
r_mcangle_other3.314
r_mcbond_it2.538
r_mcbond_other2.538
r_angle_refined_deg1.348
r_angle_other_deg0.55
r_symmetry_nbd_refined0.429
r_symmetry_xyhbond_nbd_refined0.332
r_nbd_refined0.231
r_xyhbond_nbd_refined0.222
r_symmetry_nbd_other0.191
r_nbd_other0.181
r_nbtor_refined0.179
r_symmetry_nbtor_other0.08
r_symmetry_metal_ion_refined0.063
r_chiral_restr0.058
r_bond_other_d0.015
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_metal_ion_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2167
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing