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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 1UTB PDB ENTRY 1UTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 pH 8.50
Crystal Properties Matthews coefficient Solvent content 3.5 64.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.745 α = 90 b = 107.745 β = 90 c = 298.441 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 30 99.9 0.094 13.4 9.6 50319
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 99.9 0.536 2.8 2.7
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 PDB ENTRY 1UTB 2.2 95.35 50319 2747 99.9 0.225 0.223 0.2271 0.252 0.2483 RANDOM 41.67
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] 1.29 0.64 1.29 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.89 r_scangle_it 3.468 r_scbond_it 2.062 r_angle_refined_deg 1.774 r_mcangle_it 1.695 r_angle_other_deg 0.993 r_mcbond_it 0.901 r_symmetry_hbond_refined 0.553 r_symmetry_vdw_refined 0.528 r_symmetry_vdw_other 0.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.89 r_scangle_it 3.468 r_scbond_it 2.062 r_angle_refined_deg 1.774 r_mcangle_it 1.695 r_angle_other_deg 0.993 r_mcbond_it 0.901 r_symmetry_hbond_refined 0.553 r_symmetry_vdw_refined 0.528 r_symmetry_vdw_other 0.385 r_nbd_refined 0.319 r_nbd_other 0.266 r_xyhbond_nbd_refined 0.207 r_nbtor_other 0.123 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 3479 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing