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Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA H62X, containing 3-methylhistidine at position 62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 1:1 ratio of well solution (25% PEG + 0.2 M MgCl2) and protein solution (LEA H62X at 15 mg/mL in 10 mM HEPES pH 7.5 + 75 mM NaCl).
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.778 α = 90 b = 76.733 β = 90 c = 120.07 γ = 90
Symmetry Space Group I 2 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 2022-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 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 1.7 43.59 99.7 0.056 0.06 0.02 1 18.8 8.7 24128
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 1.7 1.73 99.8 3.987 4.242 1.425 0.367 8.5
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 1.7 39.97 22846 1277 99.51 0.21101 0.20936 0.2169 0.23983 0.2212 RANDOM 44.299
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] -0.3 0.22 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.396 r_dihedral_angle_3_deg 13.114 r_dihedral_angle_4_deg 11.218 r_dihedral_angle_1_deg 7.991 r_long_range_B_refined 4.608 r_long_range_B_other 4.583 r_scangle_other 1.856 r_angle_refined_deg 1.497 r_mcangle_it 1.409 r_mcangle_other 1.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.396 r_dihedral_angle_3_deg 13.114 r_dihedral_angle_4_deg 11.218 r_dihedral_angle_1_deg 7.991 r_long_range_B_refined 4.608 r_long_range_B_other 4.583 r_scangle_other 1.856 r_angle_refined_deg 1.497 r_mcangle_it 1.409 r_mcangle_other 1.408 r_angle_other_deg 1.307 r_scbond_it 1.196 r_scbond_other 1.195 r_mcbond_it 0.969 r_mcbond_other 0.969 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 1698 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing