☰ Navigation Tabs
Crystal structure of the L. monocytogenes RmlT in complex with HEPES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES-NaOH pH 7.5
20% (w/v) PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.081 α = 90 b = 178.367 β = 93.515 c = 92.154 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 EIGER X 9M 2019-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 48.12 99.2 0.112 0.112 0.121 0.046 0.998 10.7 7 116033 49.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 98.4 1.295 1.295 1.396 0.519 0.596 1.4 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8BZ4 2.3 48.12 1.34 115974 5697 99.11 0.1944 0.193 0.193 0.2202 0.2203 60.79
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.4891 f_chiral_restr 0.6981 f_angle_d 0.5859 f_plane_restr 0.004 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19534 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 270
Software Software Software Name Purpose PHENIX refinement XDS data scaling PHASER phasing XDS data reduction