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Crystal structure of the improved version of the Genetically Encoded Green Calcium Indicator YTnC2-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.2M Sodium fluoride, 0.1M Bis-tris propane, 20% PEG 3350 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.736 α = 90 b = 65.736 β = 90 c = 315.036 γ = 120
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 EIGER X 16M 2019-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.95 46.14 100 0.313 0.321 0.071 0.992 6.5 20.2 55880
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 1.95 2 100 3.567 3.663 0.83 0.468 19.1
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 1.95 46.14 52835 2837 99.84 0.1857 0.18335 0.1884 0.22883 0.2293 RANDOM 31.401
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] 5.73 5.73 -11.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.356 r_dihedral_angle_1_deg 9.175 r_dihedral_angle_2_deg 8.835 r_long_range_B_refined 6.867 r_long_range_B_other 6.859 r_scangle_other 5.167 r_mcangle_it 4.809 r_mcangle_other 4.809 r_scbond_it 3.826 r_scbond_other 3.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.356 r_dihedral_angle_1_deg 9.175 r_dihedral_angle_2_deg 8.835 r_long_range_B_refined 6.867 r_long_range_B_other 6.859 r_scangle_other 5.167 r_mcangle_it 4.809 r_mcangle_other 4.809 r_scbond_it 3.826 r_scbond_other 3.825 r_mcbond_it 3.698 r_mcbond_other 3.69 r_angle_refined_deg 2.029 r_angle_other_deg 0.779 r_chiral_restr 0.109 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_dihedral_angle_4_deg 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 3880 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing