☰ Navigation Tabs
Structure of the Yellow-Green Fluorescent Protein mNeonGreen from Branchiostoma lanceolatum at the near physiological pH 8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG 8,000, 100mM HEPES
Crystal Properties Matthews coefficient Solvent content 1.88 34.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.27 α = 90 b = 72.27 β = 90 c = 153.97 γ = 120
Symmetry Space Group P 65 2 2
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 2015-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.953724 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 1.21 48.56 99.9 0.086 1 18.84 18.2 72944 -3 18.302
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 1.21 1.24 99.9 1.739 0.699 1.98
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 5LTP 1.21 48.56 69296 3648 99.86 0.15931 0.15798 0.167 0.18415 0.1907 RANDOM 15.704
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] 0.5 0.25 0.5 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.349 r_sphericity_free 25.135 r_dihedral_angle_4_deg 14.397 r_dihedral_angle_3_deg 11.203 r_dihedral_angle_1_deg 7.161 r_sphericity_bonded 6.573 r_long_range_B_refined 2.545 r_long_range_B_other 2.197 r_angle_refined_deg 1.593 r_scangle_other 1.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.349 r_sphericity_free 25.135 r_dihedral_angle_4_deg 14.397 r_dihedral_angle_3_deg 11.203 r_dihedral_angle_1_deg 7.161 r_sphericity_bonded 6.573 r_long_range_B_refined 2.545 r_long_range_B_other 2.197 r_angle_refined_deg 1.593 r_scangle_other 1.576 r_mcangle_other 1.435 r_mcangle_it 1.432 r_scbond_it 1.312 r_scbond_other 1.31 r_rigid_bond_restr 1.09 r_mcbond_it 1.038 r_mcbond_other 1.033 r_angle_other_deg 0.938 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1745 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement