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Crystal structure of green fluorescent protein (GFP); S65T; 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, HANGING DROP 295 0.15 M ammonium acetate, 34% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.91 35.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.937 α = 90 b = 68.887 β = 100.71 c = 60.948 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 2018-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.8856 SSRL BL12-2
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 1.15 36.49 98 0.035 1 28.4 13.5 146731 15.2
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 1.15 1.19 95.3 1.76 0.781 1.4 12.2
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 4zf3 1.15 36.49 139384 7336 98.09 0.15108 0.14968 0.1561 0.1776 0.1836 RANDOM 21.365
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] -0.03 0.18 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.212 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_4_deg 9.955 r_dihedral_angle_1_deg 6.971 r_long_range_B_refined 3.667 r_long_range_B_other 3.54 r_scangle_other 3.229 r_rigid_bond_restr 2.76 r_scbond_it 2.663 r_scbond_other 2.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.212 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_4_deg 9.955 r_dihedral_angle_1_deg 6.971 r_long_range_B_refined 3.667 r_long_range_B_other 3.54 r_scangle_other 3.229 r_rigid_bond_restr 2.76 r_scbond_it 2.663 r_scbond_other 2.662 r_mcangle_it 2.343 r_mcangle_other 2.343 r_mcbond_it 1.909 r_mcbond_other 1.883 r_angle_refined_deg 1.672 r_angle_other_deg 1.463 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 3568 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing