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Crystal structure of the ribose operon repressor, RbsR, bound to ribose operon
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 6.5 293.15 0.2 M sodium sulfate, 0.1 M bis-tris-propane (pH 6.5), and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.53 α = 90 b = 125.53 β = 90 c = 122.31 γ = 120
Symmetry Space Group P 31 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 0.978560 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 2.1 43.84 94.1 0.045 0.999 15.7 30.5 47896
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 2.1 2.33 0.184 1.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 43.84 45573 2323 73.51 0.1937 0.19214 0.22327 0.2017 RANDOM 59.92
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] 0.63 0.31 0.63 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.006 r_long_range_B_refined 9.886 r_long_range_B_other 9.886 r_scangle_other 7.86 r_dihedral_angle_1_deg 6.128 r_mcangle_it 6.103 r_mcangle_other 6.103 r_scbond_it 5.414 r_scbond_other 5.276 r_mcbond_it 4.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.006 r_long_range_B_refined 9.886 r_long_range_B_other 9.886 r_scangle_other 7.86 r_dihedral_angle_1_deg 6.128 r_mcangle_it 6.103 r_mcangle_other 6.103 r_scbond_it 5.414 r_scbond_other 5.276 r_mcbond_it 4.249 r_mcbond_other 4.249 r_angle_refined_deg 1.058 r_angle_other_deg 0.37 r_chiral_restr 0.045 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5126 Nucleic Acid Atoms 1232 Solvent Atoms 58 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement xia2 data reduction STARANISO data scaling Aimless data scaling PHASER phasing