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Crystal structure of green fluorescent protein (GFP); S65T, Y66(3-ClY); ih 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, SITTING DROP 295 0.15 M ammonium acetate, 30% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.91 35.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.22 α = 90 b = 68.73 β = 100.57 c = 60.88 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 EIGER X 16M 2018-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.9795 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.25 36.52 96.9 0.058 1 27.4 23 113139 16.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.28 93.6 1.65 0.721 1.5 10.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4zf3 1.25 36.52 107482 5657 96.93 0.12834 0.12677 0.15837 0.169 RANDOM 21.679
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] 0.45 0.18 -0.66 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.64 r_dihedral_angle_3_deg 13.241 r_dihedral_angle_4_deg 9.808 r_dihedral_angle_1_deg 6.941 r_rigid_bond_restr 5.256 r_long_range_B_refined 4.69 r_long_range_B_other 4.32 r_mcangle_it 3.841 r_mcangle_other 3.841 r_scangle_other 3.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.64 r_dihedral_angle_3_deg 13.241 r_dihedral_angle_4_deg 9.808 r_dihedral_angle_1_deg 6.941 r_rigid_bond_restr 5.256 r_long_range_B_refined 4.69 r_long_range_B_other 4.32 r_mcangle_it 3.841 r_mcangle_other 3.841 r_scangle_other 3.655 r_mcbond_it 3.539 r_mcbond_other 3.539 r_scbond_it 2.971 r_scbond_other 2.971 r_angle_refined_deg 1.616 r_angle_other_deg 1.429 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3626 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing