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Superfolder green fluorescent protein (sfGFP) exhibiting p-(phenylazo)-L-phenylalanine (Pap) at position 39 in complex with alpha-cyclodextrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 3 M sodium chloride, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.27 α = 90 b = 69.27 β = 90 c = 115.35 γ = 90
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 EIGER2 X CdTe 16M 2025-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97630 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.05 30.24 96.6 0.136 0.995 14.32 3.9 32957
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 2.05 2.15 0.822 0.788
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.05 30.24 31308 1648 96.7 0.19005 0.18804 0.1956 0.22825 0.2378 RANDOM 28.75
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] 0.4 0.4 -0.8
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 18.979 r_long_range_B_other 18.535 r_long_range_B_refined 18.49 r_scbond_it 16.842 r_scbond_other 16.84 r_dihedral_angle_3_deg 13.662 r_mcangle_it 11.011 r_mcangle_other 11.009 r_mcbond_it 8.698 r_mcbond_other 8.692
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 18.979 r_long_range_B_other 18.535 r_long_range_B_refined 18.49 r_scbond_it 16.842 r_scbond_other 16.84 r_dihedral_angle_3_deg 13.662 r_mcangle_it 11.011 r_mcangle_other 11.009 r_mcbond_it 8.698 r_mcbond_other 8.692 r_dihedral_angle_1_deg 8.528 r_dihedral_angle_2_deg 3.399 r_angle_refined_deg 1.212 r_angle_other_deg 0.462 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3569 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction