8BAW | pdb_00008baw

X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - 5-LICAM siderophore analogue complex.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Morpheus 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 coefficientSolvent content
2.0740.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.395α = 90
b = 34.432β = 92.889
c = 119.109γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2020-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.93622DiamondI03

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
11.4767.499.80.040.0480.0260.99914.66.593663
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)
11.471.52.863.4231.860.4326.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE8PBX1.47167.493643469899.7910.1820.17970.190.23260.2442.224
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]
2.02-1.192-1.9410.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.302
r_dihedral_angle_6_deg15.281
r_lrange_other9.142
r_lrange_it9.141
r_scangle_it9.136
r_scangle_other9.135
r_rigid_bond_restr8.281
r_scbond_it8.127
r_scbond_other8.125
r_mcangle_it8.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.302
r_dihedral_angle_6_deg15.281
r_lrange_other9.142
r_lrange_it9.141
r_scangle_it9.136
r_scangle_other9.135
r_rigid_bond_restr8.281
r_scbond_it8.127
r_scbond_other8.125
r_mcangle_it8.012
r_mcangle_other8.012
r_mcbond_it7.861
r_mcbond_other7.852
r_dihedral_angle_1_deg6.326
r_dihedral_angle_2_deg3.784
r_angle_refined_deg1.345
r_angle_other_deg0.464
r_symmetry_nbd_refined0.243
r_nbd_refined0.225
r_symmetry_xyhbond_nbd_refined0.215
r_xyhbond_nbd_refined0.214
r_symmetry_nbd_other0.189
r_nbd_other0.181
r_nbtor_refined0.178
r_symmetry_nbtor_other0.079
r_chiral_restr0.067
r_symmetry_xyhbond_nbd_other0.053
r_xyhbond_nbd_other0.051
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4357
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing