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Crystal structure of a response regulator receiver protein from Burkholderia phymatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BRI 5BRI, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 BuphA.00051.b.B1.PS37982 at 35 mg/mL against MCSG1 screen condition E4, 0.2 M Li2SO4, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with 20% EG as cryo-protectant
Crystal Properties Matthews coefficient Solvent content 2.31 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.39 α = 90 b = 103.84 β = 90 c = 55.47 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 300 mm CCD 2016-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 50 99.7 0.062 0.999 19.51 3.5 6748 -3 47.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 100 0.567 0.907 3.75
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 5BRI, chain A 2.401 37.906 1.35 6743 707 99.7 0.2086 0.2012 0.2051 0.2693 0.2723 62.383
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 15.627 f_angle_d 0.85 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1065 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing