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Crystal structure of the transcription regulator PbrR691 from Ralstonia metallidurans CH34 in complex with Lead(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 Tacsimate, HEPES, PEG3350
Crystal Properties Matthews coefficient Solvent content 3.12 60.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.938 α = 109.33 b = 67.903 β = 89.82 c = 89.723 γ = 90.32
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 30 95.9 0.11 23.5 3.2 88839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 94.2 0.42 5.3 3
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 5D07 2.01 30 84363 4470 94.87 0.17847 0.17661 0.1854 0.21356 0.2207 RANDOM 28.445
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] -1.3 -0.47 -0.31 -2.29 0.48 2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_sphericity_free 27.899 r_dihedral_angle_4_deg 15.879 r_dihedral_angle_3_deg 15.213 r_sphericity_bonded 9.731 r_rigid_bond_restr 4.482 r_dihedral_angle_1_deg 4.421 r_long_range_B_refined 4.015 r_long_range_B_other 3.846 r_scangle_other 3.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_sphericity_free 27.899 r_dihedral_angle_4_deg 15.879 r_dihedral_angle_3_deg 15.213 r_sphericity_bonded 9.731 r_rigid_bond_restr 4.482 r_dihedral_angle_1_deg 4.421 r_long_range_B_refined 4.015 r_long_range_B_other 3.846 r_scangle_other 3.494 r_scbond_it 2.889 r_scbond_other 2.881 r_mcangle_it 2.716 r_mcangle_other 2.715 r_mcbond_other 2.094 r_mcbond_it 2.093 r_angle_other_deg 1.581 r_angle_refined_deg 1.361 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8159 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing