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Crystal structure of DltE from L. plantarum, tartare bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, ammonium tartrate
Crystal Properties Matthews coefficient Solvent content 2.7 54.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.69 α = 90 b = 103.73 β = 90 c = 152.529 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2018-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 46.384 99.5 0.05 0.999 14.5 4.5 56946
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.564 0.787 2.4
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 8AGR 1.95 46.384 56871 2810 99.338 0.184 0.1825 0.1924 0.2211 0.2263 30.377
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] 0.011 -0.001 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.935 r_dihedral_angle_2_deg 15.337 r_dihedral_angle_3_deg 15.227 r_lrange_it 7.012 r_lrange_other 7.011 r_dihedral_angle_1_deg 6.226 r_scangle_it 5.716 r_scangle_other 5.715 r_scbond_it 3.791 r_scbond_other 3.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.935 r_dihedral_angle_2_deg 15.337 r_dihedral_angle_3_deg 15.227 r_lrange_it 7.012 r_lrange_other 7.011 r_dihedral_angle_1_deg 6.226 r_scangle_it 5.716 r_scangle_other 5.715 r_scbond_it 3.791 r_scbond_other 3.787 r_mcangle_it 3.299 r_mcangle_other 3.299 r_mcbond_it 2.53 r_mcbond_other 2.529 r_angle_refined_deg 1.433 r_angle_other_deg 0.869 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.218 r_symmetry_nbd_other 0.196 r_nbd_other 0.188 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.067 r_bond_other_d 0.036 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5006 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing