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Crystal structure of the transcriptional regulator CadR from P. putida in complex with 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 277 MPEG 2000, potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.15 60.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.967 α = 90 b = 54.541 β = 100.37 c = 86.259 γ = 90
Symmetry Space Group P 1 21 1
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 2012-11-08 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 2.8 30 99.5 0.1 15.9 5.8 15413
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 2.8 2.9 99.6 0.51 3.9 5
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 2.8 30 14632 773 98.87 0.20654 0.20407 0.2084 0.2539 0.2539 RANDOM 67.28
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] -3.01 -0.95 -7.25 9.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.456 r_dihedral_angle_4_deg 20.947 r_dihedral_angle_3_deg 17.776 r_long_range_B_refined 13.296 r_long_range_B_other 13.295 r_scangle_other 9.967 r_mcangle_other 6.291 r_mcangle_it 6.288 r_scbond_it 6.218 r_scbond_other 6.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.456 r_dihedral_angle_4_deg 20.947 r_dihedral_angle_3_deg 17.776 r_long_range_B_refined 13.296 r_long_range_B_other 13.295 r_scangle_other 9.967 r_mcangle_other 6.291 r_mcangle_it 6.288 r_scbond_it 6.218 r_scbond_other 6.217 r_dihedral_angle_1_deg 5.86 r_mcbond_it 4.077 r_mcbond_other 4.064 r_angle_refined_deg 1.36 r_angle_other_deg 1.316 r_chiral_restr 0.078 r_bond_refined_d 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1937 Nucleic Acid Atoms 1101 Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing