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Crystal structure of response regulator AdeR DNA binding domain in complex with an intercistronic region
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium citrate dibasic, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.51 α = 101.96 b = 71.38 β = 104.53 c = 78.36 γ = 101.86
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS DECTRIS PILATUS3 S 6M 2016-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.98 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.75 43.821 97.95 9.97 3.6 27914
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 (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 5X5J 2.75 43.821 21666 2000 83.03 0.27933 0.27781 0.2737 0.2958 0.2932 RANDOM 58.275
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] -2.18 5.79 -0.71 3.69 -0.27 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.831 r_dihedral_angle_4_deg 20.818 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_1_deg 6.825 r_angle_refined_deg 1.548 r_angle_other_deg 1.282 r_chiral_restr 0.109 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.831 r_dihedral_angle_4_deg 20.818 r_dihedral_angle_3_deg 16.727 r_dihedral_angle_1_deg 6.825 r_angle_refined_deg 1.548 r_angle_other_deg 1.282 r_chiral_restr 0.109 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4653 Nucleic Acid Atoms 2007 Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing