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Structure of the Pfr form of a canonical phytochrome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9C 2O9C and 4Q0J experimental model PDB 4Q0J 2O9C and 4Q0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 PEG 3350, sodium chloride, ethylene glycol, MOPS, ammonium acetate, fructose, glucose, sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.28 71.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.399 α = 90 b = 192.747 β = 90 c = 225.071 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 CCD MARMOSAIC 225 mm CCD 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.976 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 3.31 48.8 99.8 0.242 0.054 0.998 22.4 20.6 55199 116.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.31 3.48 99.6 3.616 0.793 0.469 1.4 21.1 4464
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 2O9C and 4Q0J 3.31 48.8 1.36 51713 1884 87.92 0.1976 0.1963 0.2009 0.2317 0.2336
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 16.176 f_angle_d 0.602 f_chiral_restr 0.038 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14715 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 192
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data scaling XDS data reduction