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Crystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized in dark, measured illuminated.
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 = 43.426 α = 90 b = 51.852 β = 90 c = 80.381 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 2020-06-10 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 43.57 99.7 0.116 0.129 0.055 0.996 10.9 5.2 16065 9.6
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 99.9 0.772 0.881 0.418 0.636 1.9 4.2
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 40.223 16016 815 99.565 0.161 0.1613 0.1606 0.1723 0.2154 0.1815 Random selection 17.705
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] 0.482 -0.476 -0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.37 r_dihedral_angle_other_3_deg 23.857 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 14.785 r_lrange_it 5.808 r_dihedral_angle_1_deg 5.774 r_lrange_other 5.567 r_scangle_it 3.489 r_scangle_other 3.487 r_mcangle_it 2.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.37 r_dihedral_angle_other_3_deg 23.857 r_dihedral_angle_4_deg 18.015 r_dihedral_angle_3_deg 14.785 r_lrange_it 5.808 r_dihedral_angle_1_deg 5.774 r_lrange_other 5.567 r_scangle_it 3.489 r_scangle_other 3.487 r_mcangle_it 2.481 r_mcangle_other 2.48 r_scbond_other 2.272 r_scbond_it 2.271 r_angle_other_deg 2.263 r_angle_refined_deg 1.667 r_mcbond_it 1.632 r_mcbond_other 1.631 r_nbd_refined 0.231 r_symmetry_nbd_other 0.218 r_nbd_other 0.206 r_symmetry_xyhbond_nbd_refined 0.197 r_xyhbond_nbd_refined 0.195 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.167 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.072 r_bond_refined_d 0.037 r_bond_other_d 0.032 r_gen_planes_other 0.016 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1602 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection XDS data reduction XSCALE data scaling MOLREP phasing Coot model building