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Crystal structure of DltE from L. plantarum, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG MME 5K, Tris pH8.5, LiSO4, ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.35 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.874 α = 90 b = 95.719 β = 96.26 c = 68.013 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2018-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.86 47.86 99.9 0.12 6.4 4.5 64951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.9 0.441 2
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 3WWX 1.86 47.796 64922 3142 99.826 0.168 0.1663 0.1755 0.2027 0.2103 14.051
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] -0.013 0.008 0.006 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.061 r_dihedral_angle_3_deg 14.684 r_dihedral_angle_2_deg 8.798 r_dihedral_angle_1_deg 6.172 r_lrange_it 5.529 r_lrange_other 5.528 r_scangle_it 3.806 r_scangle_other 3.806 r_scbond_it 2.477 r_scbond_other 2.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.061 r_dihedral_angle_3_deg 14.684 r_dihedral_angle_2_deg 8.798 r_dihedral_angle_1_deg 6.172 r_lrange_it 5.529 r_lrange_other 5.528 r_scangle_it 3.806 r_scangle_other 3.806 r_scbond_it 2.477 r_scbond_other 2.477 r_mcangle_other 1.889 r_mcangle_it 1.888 r_angle_refined_deg 1.353 r_mcbond_it 1.291 r_mcbond_other 1.287 r_angle_other_deg 0.712 r_nbd_other 0.267 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.225 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.161 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.067 r_bond_other_d 0.031 r_xyhbond_nbd_other 0.016 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5058 Nucleic Acid Atoms Solvent Atoms 845 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing