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Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state (I0b).
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 3.92 68.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.192 α = 90 b = 184.192 β = 90 c = 181.633 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 2019-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.24026 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 2.2 92.27 100 0.957 16.4 100.8 92007
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 2.2 2.26 0.043
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 2.2 92.27 89992 1999 99.98 0.21382 0.21321 0.221 0.24145 0.2411 RANDOM 58.385
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] -0.51 -0.26 -0.51 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.131 r_dihedral_angle_4_deg 15.242 r_dihedral_angle_3_deg 13.388 r_dihedral_angle_1_deg 5.642 r_long_range_B_refined 5.599 r_long_range_B_other 5.549 r_scangle_other 3.431 r_mcangle_it 3.215 r_mcangle_other 3.215 r_scbond_other 1.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.131 r_dihedral_angle_4_deg 15.242 r_dihedral_angle_3_deg 13.388 r_dihedral_angle_1_deg 5.642 r_long_range_B_refined 5.599 r_long_range_B_other 5.549 r_scangle_other 3.431 r_mcangle_it 3.215 r_mcangle_other 3.215 r_scbond_other 1.976 r_scbond_it 1.974 r_mcbond_it 1.895 r_mcbond_other 1.895 r_angle_refined_deg 1.213 r_angle_other_deg 1.148 r_chiral_restr 0.04 r_gen_planes_other 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_bond_refined_d 0.002 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 7481 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction PRIME data scaling PHASER phasing Coot model building PHENIX refinement