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Structure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter P1flhDC in the presence of phosphomimetic BeF3-
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 1.5M ammonium sulfate, 1.6% glycerol and 0.8M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 4.41 72.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.22 α = 90 b = 183.22 β = 90 c = 84.143 γ = 120
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 S 6M 2017-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 3.4 74.34 99.9 0.053 0.06 0.028 0.998 11.8 4.8 14477
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 3.4 3.67 99.9 0.473 0.532 0.241 0.963 4.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5O8Z 3.4 57.79 13780 694 99.88 0.2407 0.2389 0.2456 0.2735 0.2754 RANDOM 169.022
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] -14.12 -7.06 -14.12 45.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.788 r_dihedral_angle_3_deg 15.773 r_dihedral_angle_4_deg 12.768 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.2 r_angle_other_deg 1.132 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.788 r_dihedral_angle_3_deg 15.773 r_dihedral_angle_4_deg 12.768 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.2 r_angle_other_deg 1.132 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2836 Nucleic Acid Atoms 902 Solvent Atoms 5 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing