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Crystal structure of Catabolite repressor acivator from E. coli in complex with sulisobenzone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 HEPES, MgCl2, PEG 4000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.043 α = 90 b = 109.241 β = 90 c = 122.957 γ = 90
Symmetry Space Group P 2 21 21
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 R 4M 2022-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.973 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.05 43.08 98.4 0.056 0.056 0.969 17.6 1.8 11380
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.26 0.395 0.395 0.677
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 3.05 43.08 10785 594 97.77 0.23645 0.23404 0.27746 0.2769 RANDOM 70.891
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] -0.16 2.03 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.251 r_dihedral_angle_1_deg 5.934 r_long_range_B_refined 4.353 r_long_range_B_other 4.353 r_dihedral_angle_2_deg 3.445 r_mcangle_it 2.313 r_mcangle_other 2.313 r_scangle_other 1.843 r_mcbond_it 1.28 r_mcbond_other 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.251 r_dihedral_angle_1_deg 5.934 r_long_range_B_refined 4.353 r_long_range_B_other 4.353 r_dihedral_angle_2_deg 3.445 r_mcangle_it 2.313 r_mcangle_other 2.313 r_scangle_other 1.843 r_mcbond_it 1.28 r_mcbond_other 1.28 r_scbond_it 0.966 r_scbond_other 0.966 r_angle_refined_deg 0.765 r_angle_other_deg 0.277 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4429 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing