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Crystal structure of the ribose operon repressor, RbsR, bound to ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293.15 0.2 M sodium malonate (pH 4.0) and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.461 α = 90 b = 87.353 β = 100.378 c = 130.942 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 EIGER X 9M 2023-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.979493 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.07 33.82 92.1 0.118 0.985 4.8 3.5 72942
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.367 0.573
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.07 33.82 70230 3661 61.43 0.19361 0.19147 0.2005 0.23438 0.2399 RANDOM 45.886
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] -0.3 -0.13 0.34 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.553 r_long_range_B_other 12.832 r_long_range_B_refined 12.817 r_scangle_other 10.905 r_mcangle_it 8.03 r_mcangle_other 8.03 r_scbond_it 7.904 r_scbond_other 7.904 r_dihedral_angle_1_deg 7.078 r_mcbond_it 5.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.553 r_long_range_B_other 12.832 r_long_range_B_refined 12.817 r_scangle_other 10.905 r_mcangle_it 8.03 r_mcangle_other 8.03 r_scbond_it 7.904 r_scbond_other 7.904 r_dihedral_angle_1_deg 7.078 r_mcbond_it 5.565 r_mcbond_other 5.565 r_angle_refined_deg 1.247 r_angle_other_deg 0.438 r_chiral_restr 0.061 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13378 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling STARANISO data scaling PHASER phasing