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Crystal structure of the transcription regulator CadR N81M mutant 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 6JGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 HEPES, sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 4.62 73.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.435 α = 90 b = 126.435 β = 90 c = 93.783 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 2013-10-16 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 2.95 30 99.7 0.09 20.1 6.3 17117
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 2.95 3.06 99.8 0.8 2.4 6.3
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 6JGX 2.95 30 17117 912 99.64 0.20504 0.20244 0.2044 0.25293 0.2474 RANDOM 90.174
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] -4.5 -2.25 -4.5 14.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.949 r_dihedral_angle_3_deg 17.687 r_dihedral_angle_4_deg 17.257 r_long_range_B_other 14.476 r_long_range_B_refined 14.474 r_scangle_other 11.766 r_mcangle_it 9.386 r_mcangle_other 9.382 r_scbond_it 8.262 r_scbond_other 8.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.949 r_dihedral_angle_3_deg 17.687 r_dihedral_angle_4_deg 17.257 r_long_range_B_other 14.476 r_long_range_B_refined 14.474 r_scangle_other 11.766 r_mcangle_it 9.386 r_mcangle_other 9.382 r_scbond_it 8.262 r_scbond_other 8.262 r_mcbond_it 6.228 r_mcbond_other 6.225 r_dihedral_angle_1_deg 5.848 r_angle_refined_deg 1.383 r_angle_other_deg 1.235 r_chiral_restr 0.073 r_bond_refined_d 0.009 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 2134 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