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Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I1 intermediate state.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 279 1.0 - 2.2 M ammonium sulphate, 2 - 12% PEG 1000, 0.1 M HEPES pH 6.8 - 7.7, 0.025% low-melt agarose
Crystal Properties Matthews coefficient Solvent content 3.98 69.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.086 α = 90 b = 185.086 β = 90 c = 182.279 γ = 120
Symmetry Space Group P 63 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 298 CCD RAYONIX MX170-HS 2018-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.30042 SLAC LCLS MFX
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 2.54 25.41 99.8 0.841 24.3 98.4 61030
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 2.54 2.61 0.062
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.54 25.41 57572 1957 97.55 0.20663 0.20563 0.2101 0.23574 0.2393 RANDOM 66.359
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] -0.62 -0.31 -0.62 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.06 r_dihedral_angle_4_deg 14.718 r_dihedral_angle_3_deg 13.407 r_long_range_B_refined 7.002 r_long_range_B_other 6.983 r_dihedral_angle_1_deg 5.456 r_scangle_other 4.225 r_mcangle_it 4.066 r_mcangle_other 4.065 r_scbond_other 2.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.06 r_dihedral_angle_4_deg 14.718 r_dihedral_angle_3_deg 13.407 r_long_range_B_refined 7.002 r_long_range_B_other 6.983 r_dihedral_angle_1_deg 5.456 r_scangle_other 4.225 r_mcangle_it 4.066 r_mcangle_other 4.065 r_scbond_other 2.431 r_scbond_it 2.43 r_mcbond_it 2.424 r_mcbond_other 2.424 r_angle_refined_deg 1.304 r_angle_other_deg 1.156 r_chiral_restr 0.041 r_gen_planes_other 0.02 r_gen_planes_refined 0.008 r_bond_refined_d 0.003 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7485 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction PRIME data scaling PHASER phasing PHENIX refinement Coot model building