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Red fluorescent protein from Diadumene lineata
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 3.0 M Ammonium Sulfate,
0.1 M Immidazole,
2.5 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.929 α = 90 b = 75.394 β = 90 c = 118.955 γ = 90
Symmetry Space Group I 2 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 100 PIXEL DECTRIS PILATUS3 S 6M 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 43.65 100 0.068 13 6.6 26779
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.66 0.788 2.1
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 3vk1 1.63 20.001 26766 1398 99.866 0.173 0.1711 0.1772 0.2054 0.2126 23.948
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] 3.036 0.328 -3.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.063 r_dihedral_angle_4_deg 17.302 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_1_deg 7.304 r_lrange_it 4.942 r_lrange_other 4.904 r_scangle_it 4.135 r_scangle_other 4.129 r_scbond_it 2.829 r_scbond_other 2.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.063 r_dihedral_angle_4_deg 17.302 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_1_deg 7.304 r_lrange_it 4.942 r_lrange_other 4.904 r_scangle_it 4.135 r_scangle_other 4.129 r_scbond_it 2.829 r_scbond_other 2.827 r_mcangle_it 2.404 r_mcangle_other 2.403 r_mcbond_it 1.817 r_mcbond_other 1.817 r_angle_refined_deg 1.674 r_angle_other_deg 1.37 r_nbd_refined 0.264 r_symmetry_nbd_refined 0.261 r_nbd_other 0.255 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1742 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHENIX refinement