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X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - apo form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Index D3: 0.1M HEPES, pH 7.0, 30%
Jeffamine ED 2001, pH 7.0. No cryo.
Crystal Properties Matthews coefficient Solvent content 26.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.519 α = 81.566 b = 35.725 β = 83.242 c = 52.29 γ = 65.06
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 PILATUS3 6M 2018-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 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 1.42 32.225 94.9 0.033 0.046 0.033 0.998 5.8 2 37722
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 1.42 1.44 0.323 0.457 0.323 0.862 1.7
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 3zkw 1.42 32.225 37657 1940 94.67 0.169 0.1655 0.1633 0.2281 0.228 28.729
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] 0.43 0.076 1.675 -0.664 -1.253 0.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.887 r_dihedral_angle_6_deg 15.737 r_dihedral_angle_2_deg 9.768 r_lrange_other 7.156 r_lrange_it 7.152 r_scangle_it 6.871 r_scangle_other 6.469 r_dihedral_angle_1_deg 6.4 r_scbond_it 6.227 r_rigid_bond_restr 6.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.887 r_dihedral_angle_6_deg 15.737 r_dihedral_angle_2_deg 9.768 r_lrange_other 7.156 r_lrange_it 7.152 r_scangle_it 6.871 r_scangle_other 6.469 r_dihedral_angle_1_deg 6.4 r_scbond_it 6.227 r_rigid_bond_restr 6.212 r_scbond_other 5.813 r_mcangle_it 5.43 r_mcangle_other 5.428 r_mcbond_other 4.417 r_mcbond_it 4.415 r_angle_refined_deg 1.377 r_angle_other_deg 0.48 r_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.221 r_symmetry_nbd_other 0.193 r_symmetry_nbd_refined 0.193 r_nbd_other 0.182 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing