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Crystal structure of VNAR aGFP14 in complex with GFP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PPK experimental model PDB 7FBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 291 18%(w/v) PEG8000 0.1M Na/K PO4 pH6.8
Crystal Properties Matthews coefficient Solvent content 2.19 43.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.449 α = 90 b = 102.797 β = 116.33 c = 66.62 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 9M 2022-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97902 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 102.8 99.4 0.072 10.3 5.8 51988 27.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 92.7 0.523 2.5 3.8
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 4PPK, 7FBJ 1.95 59.71 49389 2536 99.3 0.189 0.186 0.1966 0.242 0.2509 RANDOM 31.79
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] 1.89 -0.63 2.43 -2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.185 r_dihedral_angle_3_deg 18.171 r_dihedral_angle_4_deg 16.281 r_long_range_B_refined 7.267 r_long_range_B_other 7.26 r_dihedral_angle_1_deg 6.938 r_scangle_other 5.545 r_mcangle_it 3.644 r_mcangle_other 3.644 r_scbond_it 3.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.185 r_dihedral_angle_3_deg 18.171 r_dihedral_angle_4_deg 16.281 r_long_range_B_refined 7.267 r_long_range_B_other 7.26 r_dihedral_angle_1_deg 6.938 r_scangle_other 5.545 r_mcangle_it 3.644 r_mcangle_other 3.644 r_scbond_it 3.498 r_scbond_other 3.498 r_mcbond_it 2.512 r_mcbond_other 2.511 r_angle_refined_deg 1.514 r_angle_other_deg 1.319 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5373 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction