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Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.8 290 2.5% PEG8K, 8% Etilenglicol, 0.1M MES pH6.8, Rap 10mg/mL, 1:5 RAP:Phr (QKGMY)
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.67 α = 90 b = 93.282 β = 94.97 c = 167.687 γ = 90
Symmetry Space Group C 1 2 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 6M KB mirrors, Si coated 2016-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.12712 ALBA XALOC
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 2.45 45.424 95.9 0.039 0.053 0.037 0.995 14 2.2 44873 92.7
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 2.45 2.492 2.8 0.788 1.074 0.759 0.622 1.3 3.2
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 THROUGHOUT 6T3H 2.45 45.424 1.34 44849 2338 67.94 0.2051 0.202 0.2035 0.2621 0.2596 68.561
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 12.851 f_angle_d 1.612 f_chiral_restr 0.081 f_bond_d 0.011 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12251 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing