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Structure of the Yellow-Green Fluorescent Protein mNeonGreen from Branchiostoma lanceolatum at the acidic pH 4.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 6.8mM CYMAL-7, 14% PEG 20,000, 100mM Sodium Citrate Tribasic Dihydrate
Crystal Properties Matthews coefficient Solvent content 1.92 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.87 α = 90 b = 127.6 β = 90 c = 146.84 γ = 90
Symmetry Space Group P 21 21 21
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-F 2014-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 46.34 96.2 0.042 0.999 13.78 4.3 291629 -3 29.915
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 96 0.582 0.632 1.58
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 4JF9 1.7 46.34 147297 7754 98.86 0.18715 0.18587 0.1938 0.21113 0.2156 RANDOM 27.384
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] 0.12 -0.35 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 15.201 r_dihedral_angle_3_deg 11.431 r_dihedral_angle_1_deg 6.857 r_long_range_B_refined 5.212 r_long_range_B_other 5.212 r_angle_refined_deg 1.499 r_mcangle_it 1.15 r_mcangle_other 1.15 r_scangle_other 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 15.201 r_dihedral_angle_3_deg 11.431 r_dihedral_angle_1_deg 6.857 r_long_range_B_refined 5.212 r_long_range_B_other 5.212 r_angle_refined_deg 1.499 r_mcangle_it 1.15 r_mcangle_other 1.15 r_scangle_other 1.027 r_angle_other_deg 0.863 r_mcbond_it 0.64 r_mcbond_other 0.64 r_scbond_it 0.587 r_scbond_other 0.587 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 10684 Nucleic Acid Atoms Solvent Atoms 910 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing