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Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-I1Y), H148D; circular permutant (50-51)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 50 mM sodium acetate, pH 5.0, 100 mM NaCl, 7-8% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.92 35.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.81 α = 90 b = 68.69 β = 99.762 c = 61.64 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 100 PIXEL DECTRIS PILATUS 6M 2017-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 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 1.65 36.182 98.3 0.07952 0.08748 0.0359 0.999 13.08 5.7 50444 21.23
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 1.65 1.709 95.58 0.9559 1.057 0.4425 0.656 1.61 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4zf3 1.65 36.182 1.36 50438 2523 98.3 0.157 0.1559 0.1577 0.1776 0.18
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 15.121 f_angle_d 0.87 f_chiral_restr 0.061 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3590 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing