☰ Navigation Tabs
Crystal structure of the transcriptional regulator CadR from P. putida in complex with Zinc(II) and DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 MPEG 2000, magnesium chloride, potassium bromide
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.09 α = 81.03 b = 71.329 β = 83.52 c = 98.797 γ = 73.85
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 2013-05-11 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 2.9 40 96.9 0.12 7.3 2.2 38729
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 2.9 3 97.2 0.51 2.7 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 (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 6JGV 2.9 30 36785 1939 95.28 0.21375 0.21158 0.2138 0.25443 0.2533 RANDOM 60.845
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] -2.13 0.62 0.79 -2.84 -0.26 5.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.432 r_dihedral_angle_4_deg 20.239 r_dihedral_angle_3_deg 17.402 r_long_range_B_refined 12.908 r_long_range_B_other 12.907 r_scangle_other 10 r_mcangle_it 7.455 r_mcangle_other 7.455 r_scbond_it 6.495 r_scbond_other 6.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.432 r_dihedral_angle_4_deg 20.239 r_dihedral_angle_3_deg 17.402 r_long_range_B_refined 12.908 r_long_range_B_other 12.907 r_scangle_other 10 r_mcangle_it 7.455 r_mcangle_other 7.455 r_scbond_it 6.495 r_scbond_other 6.495 r_dihedral_angle_1_deg 6.162 r_mcbond_it 4.93 r_mcbond_other 4.929 r_angle_other_deg 1.711 r_angle_refined_deg 1.491 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8553 Nucleic Acid Atoms 4039 Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing