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Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF192 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 279 30 - 40% MPD, 5 - 15% PEG 8000, 0.1 M MES pH 5.5 - 9.0
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.644 α = 90 b = 93.577 β = 90 c = 173.945 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 PILATUS3 6M 2021-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
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 2.059 45.83 99.9 0.857 6 6.5 75997
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 2.059 2.11 0.201 1.5
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 2.059 45.83 72339 3718 99.82 0.18776 0.18592 0.1949 0.22409 0.231 RANDOM 33.077
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] 0.56 1.61 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.789 r_dihedral_angle_4_deg 15.012 r_dihedral_angle_3_deg 12.877 r_dihedral_angle_1_deg 6.129 r_long_range_B_refined 5.083 r_long_range_B_other 4.981 r_scangle_other 3.297 r_mcangle_it 2.662 r_mcangle_other 2.662 r_scbond_it 2.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.789 r_dihedral_angle_4_deg 15.012 r_dihedral_angle_3_deg 12.877 r_dihedral_angle_1_deg 6.129 r_long_range_B_refined 5.083 r_long_range_B_other 4.981 r_scangle_other 3.297 r_mcangle_it 2.662 r_mcangle_other 2.662 r_scbond_it 2.041 r_scbond_other 2.041 r_mcbond_it 1.696 r_mcbond_other 1.695 r_angle_refined_deg 1.326 r_angle_other_deg 1.306 r_chiral_restr 0.055 r_gen_planes_other 0.013 r_bond_other_d 0.01 r_gen_planes_refined 0.008 r_bond_refined_d 0.005 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 7547 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing