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Dimeric PAS domains of oxygen sensor FixL in complex with imidazole-bound heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JS5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 1.5 M Ammonium sulfate, 0.1 M Sodium Acetate, 10 mM Imidazole
Crystal Properties Matthews coefficient Solvent content 4.14 70.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.854 α = 90 b = 199.313 β = 90 c = 270.01 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 PIXEL DECTRIS EIGER X 9M 2019-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.85 50 99.7 0.16 0.998 10.5 7.21 117838 -3 73.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3.02 98 1.69 0.493 1.04 7.25
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.85 49.83 1.34 117838 5941 99.69 0.2174 0.2158 0.2124 0.2482 0.244 115.19
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 28.4384 f_angle_d 1.1534 f_chiral_restr 0.093 f_plane_restr 0.0082 f_bond_d 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19789 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 570
Software Software Software Name Purpose PHENIX refinement XDS data scaling Coot model building PHENIX phasing XDS data reduction