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Room temperature crystal structure of enhanced Green Fluorescent Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.5 microliters of 10 mg/mL protein was mixed with 0.5 microliters of 100 mM MES pH 6.5, 300 mM calcium acetate, and 20% (w/v) PEG 8,000 and allowed to equilibrate over a 500 microliter reservoir over several days. Large single crystals from seeding into 100 mM MES pH 6.5, 300 mM calcium acetate, and 4-10% (w/v) PEG 8,000 in the same format.
Crystal Properties Matthews coefficient Solvent content 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.533 α = 90 b = 62.83 β = 90 c = 70.636 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 PIXEL DECTRIS PILATUS 6M 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.95369 SSRL BL12-2
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 1.4 46.95 99.8 0.1674 0.1735 0.04487 0.999 9.36 14.4 48817 15.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.43 99.58 0.04439 1.043 0.362 0.94 14.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 46.95 1.34 45778 2293 99.8 0.1208 0.1194 0.1194 0.1563 0.1563 21.69
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 f_dihedral_angle_d 14.844 f_angle_d 0.9884 f_chiral_restr 0.0918 f_bond_d 0.0102 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1831 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHENIX phasing