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Crystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 20 % (w/v) methanol, 10 mM CaCl2 and 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.42 α = 90 b = 91.77 β = 90 c = 97.71 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97946 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.4 66.893 97.2 0.087 0.101 0.049 7.9 3.6 17045 17045 21.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 98.6 0.332 0.332 0.189 2.1 3.6 2485
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 FREE R-VALUE 3LOC 2.4 66.89 16147 865 96.33 0.1972 0.1945 0.2468 0.214 RANDOM 58.072
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] -0.04 1.19 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.568 r_dihedral_angle_4_deg 16.86 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 4.993 r_mcangle_it 2.772 r_mcbond_it 1.791 r_mcbond_other 1.788 r_angle_refined_deg 1.312 r_angle_other_deg 1.03 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.568 r_dihedral_angle_4_deg 16.86 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 4.993 r_mcangle_it 2.772 r_mcbond_it 1.791 r_mcbond_other 1.788 r_angle_refined_deg 1.312 r_angle_other_deg 1.03 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3086 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction