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Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG 8000, magnesium acetate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 1.97 37.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.273 α = 90 b = 64.273 β = 90 c = 84.116 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2022-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 1.1211 AichiSR BL2S1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 45.489 100 0.069 1 26.2 13.9 18446 19.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.903 0.876 3.4 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7CKV 1.75 45.489 18395 861 99.962 0.19 0.1875 0.1976 0.2311 0.2421 24.374
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] 0.274 0.274 -0.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.28 r_dihedral_angle_4_deg 14.631 r_dihedral_angle_3_deg 14.373 r_dihedral_angle_1_deg 7.094 r_lrange_it 6.26 r_lrange_other 6.24 r_scangle_it 5.027 r_scangle_other 5.025 r_scbond_it 3.285 r_scbond_other 3.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.28 r_dihedral_angle_4_deg 14.631 r_dihedral_angle_3_deg 14.373 r_dihedral_angle_1_deg 7.094 r_lrange_it 6.26 r_lrange_other 6.24 r_scangle_it 5.027 r_scangle_other 5.025 r_scbond_it 3.285 r_scbond_other 3.285 r_mcangle_it 2.948 r_mcangle_other 2.948 r_mcbond_it 2.195 r_mcbond_other 2.187 r_angle_refined_deg 1.706 r_angle_other_deg 1.449 r_symmetry_nbd_refined 0.221 r_nbd_refined 0.211 r_symmetry_nbd_other 0.183 r_nbd_other 0.179 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.122 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1438 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing