☰ Navigation Tabs
Crystal structure of the histidine kinase domain of bacteriophytochrome RpBphP2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 25% PEG3350, 0.2 M sodium chloride, 0.1 M Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.851 α = 90 b = 84.851 β = 90 c = 346.06 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 PIXEL DECTRIS EIGER X 9M 2018-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9787 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.19 50 99.5 0.041 17.8 8.6 22330 102.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 97.8 0.429 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 3.19 42.11 1.35 22330 1103 96.58 0.2238 0.2218 0.2643 0.2699
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 7.016 f_angle_d 0.924 f_chiral_restr 0.057 f_plane_restr 0.009 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3090 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data scaling AutoSol phasing HKL-2000 data reduction