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Crystal structure of the transcriptional regulator CadR from P. putida in complex with Cadmium(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 7.3 289 PEG 3350, potassium chloride, magnesium chloride, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 4.77 74.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.49 α = 90 b = 131.49 β = 90 c = 85.118 γ = 120
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 2014-10-16 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 2.7 30 98.9 0.06 26.2 6.2 22742
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 2.7 2.8 96.9 0.56 2.2 4.8
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 2.71 30 21613 1128 98.79 0.21051 0.20927 0.211 0.23347 0.2304 RANDOM 85.244
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] -2.08 -1.04 -2.08 6.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.475 r_dihedral_angle_3_deg 18.026 r_dihedral_angle_4_deg 16.62 r_long_range_B_refined 13.664 r_long_range_B_other 13.662 r_scangle_other 10.202 r_mcangle_it 9.484 r_mcangle_other 9.484 r_scbond_it 6.574 r_scbond_other 6.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.475 r_dihedral_angle_3_deg 18.026 r_dihedral_angle_4_deg 16.62 r_long_range_B_refined 13.664 r_long_range_B_other 13.662 r_scangle_other 10.202 r_mcangle_it 9.484 r_mcangle_other 9.484 r_scbond_it 6.574 r_scbond_other 6.57 r_mcbond_it 6.042 r_mcbond_other 6.03 r_dihedral_angle_1_deg 5.924 r_angle_refined_deg 1.359 r_angle_other_deg 1.172 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 2200 Nucleic Acid Atoms 896 Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing