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Deoxyribonucleoside regulator DeoR in complex with the DNA operator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQQ for residues 56-313 experimental model PDB 2W48 for residues 1-55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 292 The volume ratio of the protein/DNA solution and precipitant solution - 1:2
Precipitant solution:
50 mM sodium cacodylate, pH 6.3, 75 mM CaCl2, 25 mM MgCl2, 3.5% (v/v) PEG 2K
Crystal was cryo-protected by a quick soaking in 25% (v/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 4.22 70.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.672 α = 90 b = 166.672 β = 90 c = 331.697 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS 6M 2018-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9141 BESSY 14.1
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 3.6 50 98.9 0.748 0.993 4.86 13.1 32081 122.8
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 3.6 3.81 96.4 8.886 0.123 0.35
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.7 48.924 29634 1482 99.2 0.269 0.2655 0.3328 0.2693 172.198
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] 1.194 0.597 1.194 -3.873
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 36.36 r_scangle_it 25.467 r_mcangle_it 22.766 r_dihedral_angle_1_deg 20.224 r_dihedral_angle_3_deg 17.127 r_scbond_it 15.775 r_dihedral_angle_6_deg 15.735 r_mcbond_it 14.012 r_dihedral_angle_2_deg 5.901 r_paralell_plane_angle_deg 4.846
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 36.36 r_scangle_it 25.467 r_mcangle_it 22.766 r_dihedral_angle_1_deg 20.224 r_dihedral_angle_3_deg 17.127 r_scbond_it 15.775 r_dihedral_angle_6_deg 15.735 r_mcbond_it 14.012 r_dihedral_angle_2_deg 5.901 r_paralell_plane_angle_deg 4.846 r_angle_refined_deg 1.211 r_symmetry_nbd_refined 0.421 r_nbtor_refined 0.315 r_nbd_refined 0.253 r_symmetry_xyhbond_nbd_refined 0.229 r_chiral_restr 0.203 r_xyhbond_nbd_refined 0.188 r_ext_dist_refined_b 0.04 r_gen_planes_refined 0.015 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9792 Nucleic Acid Atoms 1464 Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing