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Crystal Structure of apo and reduced Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Crystallization buffer: 2.5M ammonium sulfate, 0.1M sodium acetate pH 4.6; Protein buffer: 20 mM Tris pH 8, 200 mM NaCl, 2mM TCEP, 2mM EDTA, 5% glycerol; SqrR 6 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.849 α = 90 b = 46.849 β = 90 c = 163.306 γ = 120
Symmetry Space Group P 61 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 CMOS RDI CMOS_8M 2017-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.072152 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.12 54.44 100 0.081 0.083 0.019 1 26.6 19.4 6628
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3PQK 2.12 28.778 0.31 6618 310 99.94 0.2253 0.2233 0.2206 0.2642 0.2576
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.402 f_angle_d 1.29 f_chiral_restr 0.054 f_bond_d 0.014 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 728 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing