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Crystal structure of DltE from L. plantarum, TCEP 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, TCEP HCl
Crystal Properties Matthews coefficient Solvent content 2.94 58.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.236 α = 90 b = 98.642 β = 105.799 c = 135.934 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 PILATUS 2M 2018-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873130 ESRF ID23-2
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 1.94 49.501 97.7 0.095 0.988 5.3 3.8 139757
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 1.94 1.97 0.395 0.811
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 1.94 49.501 139693 1994 97.569 0.184 0.1833 0.1916 0.2124 0.217 24.243
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] -0.014 -0.003 0.001 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.706 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_2_deg 6.635 r_lrange_it 6.554 r_lrange_other 6.473 r_dihedral_angle_1_deg 6.031 r_scangle_it 4.903 r_scangle_other 4.902 r_scbond_it 3.267 r_scbond_other 3.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.706 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_2_deg 6.635 r_lrange_it 6.554 r_lrange_other 6.473 r_dihedral_angle_1_deg 6.031 r_scangle_it 4.903 r_scangle_other 4.902 r_scbond_it 3.267 r_scbond_other 3.267 r_mcangle_it 3.086 r_mcangle_other 3.086 r_mcbond_it 2.286 r_mcbond_other 2.284 r_angle_refined_deg 1.397 r_angle_other_deg 0.774 r_nbd_other 0.247 r_nbd_refined 0.23 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.18 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_other 0.154 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.076 r_bond_other_d 0.036 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10510 Nucleic Acid Atoms Solvent Atoms 1210 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing