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DNA bound structure of PrgE from plasmid pCF10
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 15 % Polyethylene glycol 400, 50 mM MES pH 6.5, 80 mM Magnesium acetate, 15 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.22 61.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.776 α = 90 b = 90.043 β = 90 c = 131.848 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 EIGER2 X 16M 2023-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.67 49.74 99.75 0.1158 0.998 10.71 6.7 26266 73.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.765 99.06 2.067 0.628 0.95 7
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 (All) 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 2.67 49.74 24963 1275 99.81 0.231 0.23052 0.22939 0.2294 0.25257 0.2516 RANDOM 94.065
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] -0.54 1.24 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 6.258 r_long_range_B_refined 5.063 r_long_range_B_other 5.063 r_dihedral_angle_2_deg 3.091 r_mcangle_it 2.731 r_mcangle_other 2.731 r_scangle_other 2.586 r_mcbond_it 1.532 r_mcbond_other 1.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 6.258 r_long_range_B_refined 5.063 r_long_range_B_other 5.063 r_dihedral_angle_2_deg 3.091 r_mcangle_it 2.731 r_mcangle_other 2.731 r_scangle_other 2.586 r_mcbond_it 1.532 r_mcbond_other 1.532 r_scbond_it 1.405 r_scbond_other 1.404 r_angle_refined_deg 0.683 r_angle_other_deg 0.254 r_chiral_restr 0.035 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 3372 Nucleic Acid Atoms 315 Solvent Atoms 9 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing Coot model building