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Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA A69T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 2 microliters of protein at 20 mg/mL in 10 mM HEPES pH 7.5 + 75 mM NaCl mixed with 2 microliters of well solution containing 35% PEG 3350 + 0.3 M potassium nitrate
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.447 α = 90 b = 106.084 β = 90 c = 123.471 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 2022-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.5 48.74 99.8 0.066 0.071 0.025 1 18.3 7.8 152026
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 97.2 1.814 2.05 0.927 0.331 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 47.03 144318 7617 99.71 0.1636 0.16232 0.1716 0.18806 0.17 RANDOM 22.493
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 -0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.93 r_dihedral_angle_4_deg 14.348 r_dihedral_angle_3_deg 11.773 r_dihedral_angle_1_deg 7.783 r_long_range_B_refined 5.235 r_long_range_B_other 4.974 r_scangle_other 2.349 r_angle_refined_deg 1.769 r_scbond_it 1.58 r_scbond_other 1.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.93 r_dihedral_angle_4_deg 14.348 r_dihedral_angle_3_deg 11.773 r_dihedral_angle_1_deg 7.783 r_long_range_B_refined 5.235 r_long_range_B_other 4.974 r_scangle_other 2.349 r_angle_refined_deg 1.769 r_scbond_it 1.58 r_scbond_other 1.576 r_mcangle_it 1.487 r_mcangle_other 1.487 r_angle_other_deg 1.482 r_mcbond_it 0.976 r_mcbond_other 0.971 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 6973 Nucleic Acid Atoms Solvent Atoms 962 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing