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Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I4 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 3.88 68.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.756 α = 90 b = 183.756 β = 90 c = 180.318 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 MPCCD 2019-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.24052 SACLA BL2
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 2.3 90.32 100 0.984 13.5 506.8 79712
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 2.3 2.36 0.012
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 2.3 90.32 77705 2000 99.99 0.24947 0.24855 0.2486 0.28523 0.2797 RANDOM 58.438
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] -0.16 -0.08 -0.16 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.133 r_dihedral_angle_4_deg 14.661 r_dihedral_angle_3_deg 13.926 r_long_range_B_refined 6.585 r_long_range_B_other 6.585 r_dihedral_angle_1_deg 5.67 r_scangle_other 3.709 r_mcangle_it 3.66 r_mcangle_other 3.659 r_mcbond_it 2.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.133 r_dihedral_angle_4_deg 14.661 r_dihedral_angle_3_deg 13.926 r_long_range_B_refined 6.585 r_long_range_B_other 6.585 r_dihedral_angle_1_deg 5.67 r_scangle_other 3.709 r_mcangle_it 3.66 r_mcangle_other 3.659 r_mcbond_it 2.134 r_mcbond_other 2.134 r_scbond_it 2.121 r_scbond_other 2.121 r_angle_refined_deg 1.303 r_angle_other_deg 1.148 r_chiral_restr 0.041 r_gen_planes_other 0.014 r_gen_planes_refined 0.007 r_bond_refined_d 0.004 r_bond_other_d 0.004 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 7508 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction PRIME data scaling PHASER phasing Coot model building