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Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF205 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 2.66 53.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.411 α = 90 b = 93.542 β = 90 c = 173.757 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 EIGER X 16M 2022-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.79 41.22 99.88 0.984 10.15 6.9 114259
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 1.79 1.81 0.724
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 1.79 41.22 108532 5812 99.8 0.17914 0.17767 0.1888 0.20694 0.2143 RANDOM 28.259
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] 0.06 2.69 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.957 r_dihedral_angle_2_deg 7.572 r_dihedral_angle_1_deg 5.893 r_long_range_B_refined 5.116 r_long_range_B_other 4.888 r_scangle_other 3.019 r_mcangle_it 2.336 r_mcangle_other 2.336 r_scbond_it 1.815 r_scbond_other 1.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.957 r_dihedral_angle_2_deg 7.572 r_dihedral_angle_1_deg 5.893 r_long_range_B_refined 5.116 r_long_range_B_other 4.888 r_scangle_other 3.019 r_mcangle_it 2.336 r_mcangle_other 2.336 r_scbond_it 1.815 r_scbond_other 1.815 r_mcbond_it 1.459 r_mcbond_other 1.458 r_angle_other_deg 1.237 r_angle_refined_deg 1.085 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 7550 Nucleic Acid Atoms Solvent Atoms 975 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing