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The crystal structure of CsvR from Escherichia coli
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, SITTING DROP 293 20 %w/v PEG3350
0.15 M DL-malic 7 pH
6 %w/v Glycerol
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.613 α = 90 b = 77.601 β = 90 c = 184.947 γ = 90
Symmetry Space Group P 21 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 X 16M 2023-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
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 3.03 48.32 69.8 0.175 0.183 0.051 0.998 10.1 12.9 8763
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 3.03 3.285 16.6 2.748 2.861 0.791 0.454 1.2 13
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 3.03 48.32 8360 403 69.7 0.21641 0.21225 0.2149 0.29781 0.2877 RANDOM 147.964
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] -7.42 1.84 5.58
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.698 r_long_range_B_other 19.697 r_dihedral_angle_3_deg 18.821 r_scangle_other 11.77 r_mcangle_it 10.513 r_mcangle_other 10.511 r_dihedral_angle_1_deg 8.141 r_dihedral_angle_2_deg 7.66 r_scbond_it 6.984 r_scbond_other 6.983
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.698 r_long_range_B_other 19.697 r_dihedral_angle_3_deg 18.821 r_scangle_other 11.77 r_mcangle_it 10.513 r_mcangle_other 10.511 r_dihedral_angle_1_deg 8.141 r_dihedral_angle_2_deg 7.66 r_scbond_it 6.984 r_scbond_other 6.983 r_mcbond_it 6.343 r_mcbond_other 6.341 r_angle_refined_deg 1.608 r_angle_other_deg 0.516 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 4047 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling XDS data reduction PHASER phasing