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Crystal structure of heme binding PAS domain from one component transcription factor, FG214 reduced with dithionite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other D_1000301930 to be deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate, 0.2M 1,6-Hexanediol, 0.2M 1-Butanol
0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol, 0.4M Imidazole, 0.6M MES monohydrate, 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.35 63.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.03 α = 90 b = 65.21 β = 90 c = 105.87 γ = 90
Symmetry Space Group P 21 21 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 2025-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.648 55.523 100 0.999 11 7.4 393593 31.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.648 1.677 0.382
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 1.65 45.32 1.35 53262 2635 99.77 0.1889 0.1876 0.1904 0.2154 0.2182 38.67
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 17.0081 f_angle_d 1.1172 f_chiral_restr 0.057 f_plane_restr 0.0169 f_bond_d 0.0106
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2246 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing autoPROC data processing