☰ Navigation Tabs
Crystal structure of a bright green fluorescent protein (StayGold) with double mutations (N137A, Y187F) in jellyfish Cytaeis uchidae from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH7.5, 1.4 M Na3citrate
Crystal Properties Matthews coefficient Solvent content 2.77 55.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.086 α = 90 b = 135.086 β = 90 c = 58.427 γ = 120
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 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 1.7 19.77 99.9 0.096 12.8 6.1 67020
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 1.7 1.73 0.855
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 AlphaFold 1.7 19.77 66990 3422 99.916 0.148 0.1464 0.1589 0.1694 0.1767 19.34
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] 0.308 0.154 0.308 -0.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.605 r_dihedral_angle_4_deg 14.673 r_dihedral_angle_3_deg 12.326 r_lrange_it 7.315 r_dihedral_angle_1_deg 7.244 r_lrange_other 7.115 r_scangle_it 5.718 r_scangle_other 5.717 r_scbond_it 3.629 r_scbond_other 3.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.605 r_dihedral_angle_4_deg 14.673 r_dihedral_angle_3_deg 12.326 r_lrange_it 7.315 r_dihedral_angle_1_deg 7.244 r_lrange_other 7.115 r_scangle_it 5.718 r_scangle_other 5.717 r_scbond_it 3.629 r_scbond_other 3.624 r_mcangle_other 2.468 r_mcangle_it 2.461 r_angle_refined_deg 1.811 r_mcbond_it 1.73 r_mcbond_other 1.703 r_angle_other_deg 1.44 r_metal_ion_refined 0.311 r_symmetry_xyhbond_nbd_refined 0.257 r_nbd_other 0.213 r_symmetry_nbd_refined 0.201 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.171 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3410 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing