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Photoswitchable fluorescent protein Gamillus, off-state (pH7.0)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 Ammonium phosphate, sodium citrate, sodium chloride, HEPES, pH5.5
Crystal Properties Matthews coefficient Solvent content 5.79 78.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.711 α = 90 b = 161.711 β = 90 c = 161.711 γ = 90
Symmetry Space Group I 21 3
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 RAYONIX MX300HE 2016-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 46.682 99.7 0.064 0.069 0.999 17.34 7.408 64910 32.623
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 99.5 0.438 0.47 0.939 3.91 7.55
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 (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 5Y00 1.8 46.68 61681 3247 99.7 0.1543 0.1536 0.1658 0.1677 0.1788 RANDOM 29.584
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.266 r_dihedral_angle_4_deg 15.118 r_dihedral_angle_3_deg 12.588 r_dihedral_angle_1_deg 7.358 r_angle_refined_deg 2.939 r_angle_other_deg 1.337 r_chiral_restr 0.208 r_bond_refined_d 0.034 r_gen_planes_refined 0.018 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.266 r_dihedral_angle_4_deg 15.118 r_dihedral_angle_3_deg 12.588 r_dihedral_angle_1_deg 7.358 r_angle_refined_deg 2.939 r_angle_other_deg 1.337 r_chiral_restr 0.208 r_bond_refined_d 0.034 r_gen_planes_refined 0.018 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1813 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 484
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PDB_EXTRACT data extraction MOLREP phasing