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Structure of the Yellow Fluorescent Protein lanYFP from Branchiostoma lanceolatum at pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JF9 pdbid 4JF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.19mM CYMAL-7, 40% PEG 400, 100mM HEPES
Crystal Properties Matthews coefficient Solvent content 1.83 32.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.66 α = 90 b = 197.16 β = 90.45 c = 115.09 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-F 2014-04-30 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 2.05 49.29 99.4 0.076 0.998 13.54 3.8 217268 -3 35.092
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 2.05 2.1 99.6 0.585 0.718 2.4
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 THROUGHOUT pdbid 4JF9 2.05 49.29 206403 10864 99.37 0.22677 0.22535 0.2281 0.25371 0.2534 RANDOM 37.669
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] -0.02 -0.04 0.18 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.226 r_dihedral_angle_4_deg 14.227 r_dihedral_angle_3_deg 11.462 r_dihedral_angle_1_deg 6.205 r_long_range_B_refined 2.314 r_long_range_B_other 2.291 r_angle_refined_deg 1.296 r_angle_other_deg 0.828 r_mcangle_it 0.324 r_mcangle_other 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.226 r_dihedral_angle_4_deg 14.227 r_dihedral_angle_3_deg 11.462 r_dihedral_angle_1_deg 6.205 r_long_range_B_refined 2.314 r_long_range_B_other 2.291 r_angle_refined_deg 1.296 r_angle_other_deg 0.828 r_mcangle_it 0.324 r_mcangle_other 0.324 r_scangle_other 0.18 r_mcbond_it 0.173 r_mcbond_other 0.173 r_scbond_it 0.095 r_scbond_other 0.095 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27660 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms 16
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement