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Double mutant Y110S,F111V DntR from Burkholderia sp. strain DNT in complex with thiocyanate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UTH PDB ENTRY 1UTH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M IMIDAZOL PH 6.5 0.2M KSCN 0.9M NA ACETATE
Crystal Properties Matthews coefficient Solvent content 4.7 73.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.874 α = 90 b = 106.874 β = 90 c = 296.888 γ = 120
Symmetry Space Group P 65 2 2
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 CCD TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 67.57 97.8 0.09 18.3 8.5 50378 3 43.38
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 2.32 97.8 0.42 2.1 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UTH 2.2 67.57 47796 2582 97.1 0.208 0.207 0.237 0.2429 RANDOM 39.74
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] 0.89 0.45 0.89 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.79 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 16.576 r_dihedral_angle_1_deg 6.558 r_scangle_it 3.579 r_scbond_it 2.288 r_angle_refined_deg 1.766 r_mcangle_it 1.673 r_mcbond_it 0.915 r_symmetry_vdw_refined 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.79 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 16.576 r_dihedral_angle_1_deg 6.558 r_scangle_it 3.579 r_scbond_it 2.288 r_angle_refined_deg 1.766 r_mcangle_it 1.673 r_mcbond_it 0.915 r_symmetry_vdw_refined 0.399 r_nbtor_refined 0.303 r_nbd_refined 0.297 r_symmetry_hbond_refined 0.237 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3414 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing