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Crystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized and measured in dark.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 21% (w/v) PEG 8000, 0.22 M MgCl2, 0.11 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.96 37.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.81 α = 90 b = 51.961 β = 90 c = 81.063 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 Bruker PHOTON II HELIOS optics for MetalJet 2020-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2 70 kV 1.3418
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 1.85 30.975 95.6 0.07 0.078 0.035 0.998 13.2 4.6 15648 10.8
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 1.85 1.89 69.6 0.437 0.567 0.355 0.773 2.5 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3P7N 1.85 30.975 15608 800 95.316 0.161 0.1607 0.15986 0.171 0.21528 0.1822 Random selection 18.205
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] 0.041 -0.524 0.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.949 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_3_deg 15.557 r_dihedral_angle_1_deg 5.814 r_lrange_it 5.779 r_lrange_other 5.698 r_scangle_it 3.741 r_scangle_other 3.74 r_mcangle_it 2.528 r_mcangle_other 2.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.949 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_3_deg 15.557 r_dihedral_angle_1_deg 5.814 r_lrange_it 5.779 r_lrange_other 5.698 r_scangle_it 3.741 r_scangle_other 3.74 r_mcangle_it 2.528 r_mcangle_other 2.527 r_scbond_it 2.379 r_scbond_other 2.376 r_angle_other_deg 2.289 r_angle_refined_deg 1.727 r_mcbond_it 1.676 r_mcbond_other 1.676 r_symmetry_xyhbond_nbd_refined 0.222 r_symmetry_nbd_other 0.22 r_nbd_refined 0.208 r_nbd_other 0.193 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.166 r_symmetry_nbd_refined 0.165 r_symmetry_xyhbond_nbd_other 0.139 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.075 r_bond_other_d 0.033 r_gen_planes_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1602 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 47
Software Software Software Name Purpose PROTEUM data collection PROTEUM data reduction SADABS data scaling MOLREP phasing Coot model building REFMAC refinement