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Crystal structure of the genetically-encoded green calcium sensor icBTnC2 in its calcium bound-state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 30% MPD,20mM CaCl2 ,100 mM NaAcetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.59 65.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.697 α = 90 b = 128.697 β = 90 c = 52.737 γ = 120
Symmetry Space Group P 31 2 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 CCD MAR CCD 165 mm 2025-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.75172 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 55.73 99.9 0.973 6.7 12.9 72730
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 0.53 1.1
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 1.55 55.73 69063 3647 99.85 0.19847 0.19736 0.2069 0.21958 0.2283 RANDOM 23.069
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] -0.09 -0.05 -0.09 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.002 r_dihedral_angle_3_deg 12.553 r_long_range_B_other 10.378 r_long_range_B_refined 10.374 r_scangle_other 9.411 r_dihedral_angle_1_deg 7.883 r_scbond_it 6.892 r_scbond_other 6.89 r_mcangle_it 6.035 r_mcangle_other 6.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.002 r_dihedral_angle_3_deg 12.553 r_long_range_B_other 10.378 r_long_range_B_refined 10.374 r_scangle_other 9.411 r_dihedral_angle_1_deg 7.883 r_scbond_it 6.892 r_scbond_other 6.89 r_mcangle_it 6.035 r_mcangle_other 6.033 r_rigid_bond_restr 5.942 r_mcbond_it 4.309 r_mcbond_other 4.309 r_angle_refined_deg 1.913 r_angle_other_deg 1.034 r_chiral_restr 0.11 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.005 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction gemmi data extraction PHASER phasing