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Crystal structure of response regulator receiver protein from Burkholderia phymatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 BuphA.00051.a.B1.PS38011 at 14 mg/mL against MCSG1 screen condition C9, 0.8M LiCl, 0.1 M Tris pH 8.5, 32% PEG 4000 supplemented with 20% ethylene glycol as cryo protectant, crystal tracking ID 284229c9, unique puck LBQ7-6
Crystal Properties Matthews coefficient Solvent content 1.87 34.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.6 α = 90 b = 82.6 β = 90 c = 31.97 γ = 90
Symmetry Space Group P 43 21 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 MARMOSAIC 300 mm CCD 2016-10-12 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 1.3 50 95.8 0.061 0.999 25.89 12.2 26700 -3 9.99
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 1.3 1.33 91.7 0.416 0.955 6.3
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 THROUGHOUT 3NHZ 1.3 36.94 1.36 26662 2012 95.83 0.1409 0.1384 0.139 0.1715 0.1716 14.208
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 16.926 f_angle_d 0.845 f_chiral_restr 0.075 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 919 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 7
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction