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Crystal structure of Cyanobacteriochrome GAF domain in Pr state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 27% PEG 4000, 0.2M MgCl2, 0.1M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 1.86 33.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.73 α = 90 b = 101.334 β = 91.788 c = 41.81 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2020-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 1.12 AichiSR BL2S1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.63 41.79 99.6 0.046 0.054 0.027 0.996 13.3 3.9 36876 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.66 99.9 0.483 0.562 0.285 0.837 2.2 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3vv4 1.63 38.663 36846 1753 99.525 0.16 0.1583 0.1991 0.2037 Random selection 20.225
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] 1.14 -0.669 -0.822 -0.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.052 r_dihedral_angle_4_deg 19.451 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_other_3_deg 7.966 r_dihedral_angle_1_deg 6.629 r_lrange_it 6.578 r_lrange_other 6.46 r_scangle_it 4.444 r_scangle_other 4.443 r_scbond_other 2.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.052 r_dihedral_angle_4_deg 19.451 r_dihedral_angle_3_deg 13.173 r_dihedral_angle_other_3_deg 7.966 r_dihedral_angle_1_deg 6.629 r_lrange_it 6.578 r_lrange_other 6.46 r_scangle_it 4.444 r_scangle_other 4.443 r_scbond_other 2.892 r_scbond_it 2.891 r_mcangle_other 2.771 r_mcangle_it 2.767 r_mcbond_it 1.893 r_mcbond_other 1.885 r_angle_refined_deg 1.718 r_angle_other_deg 1.468 r_symmetry_nbd_refined 0.324 r_nbd_refined 0.224 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.182 r_nbd_other 0.18 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.17 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2273 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing