8B7X

X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - apo form.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZKW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Index D3: 0.1M HEPES, pH 7.0, 30% Jeffamine ED 2001, pH 7.0. No cryo.
Crystal Properties
Matthews coefficientSolvent content
26.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.519α = 81.566
b = 35.725β = 83.242
c = 52.29γ = 65.06
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97622DiamondI03

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
11.4232.22594.90.0330.0460.0330.9985.8237722
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)
11.421.440.3230.4570.3230.8621.7

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-VALUE3zkw1.4232.22537657194094.670.1690.16550.228128.729
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]
0.430.0761.675-0.664-1.2530.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.887
r_dihedral_angle_6_deg15.737
r_dihedral_angle_2_deg9.768
r_lrange_other7.156
r_lrange_it7.152
r_scangle_it6.871
r_scangle_other6.469
r_dihedral_angle_1_deg6.4
r_scbond_it6.227
r_rigid_bond_restr6.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.887
r_dihedral_angle_6_deg15.737
r_dihedral_angle_2_deg9.768
r_lrange_other7.156
r_lrange_it7.152
r_scangle_it6.871
r_scangle_other6.469
r_dihedral_angle_1_deg6.4
r_scbond_it6.227
r_rigid_bond_restr6.212
r_scbond_other5.813
r_mcangle_it5.43
r_mcangle_other5.428
r_mcbond_other4.417
r_mcbond_it4.415
r_angle_refined_deg1.377
r_angle_other_deg0.48
r_nbd_refined0.221
r_symmetry_xyhbond_nbd_refined0.221
r_symmetry_nbd_other0.193
r_symmetry_nbd_refined0.193
r_nbd_other0.182
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.152
r_symmetry_nbtor_other0.078
r_chiral_restr0.069
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2174
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing