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Crystal structure of the calcium indicator GCaMP6s-BrUS-145 in calcium-bounded state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.2M Sodium thiocyanate, pH 6.9, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.33 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.293 α = 90 b = 118.293 β = 90 c = 98.703 γ = 90
Symmetry Space Group P 41 21 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 RIGAKU HyPix-6000HE 2022-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.542
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 2.05 23.01 99.9 0.184 0.188 0.038 0.999 17.2 24.8 44474
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 2.05 2.11 100 1.736 1.788 0.425 0.83 17.4
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 2.05 23.01 41351 2167 97.87 0.21264 0.21057 0.2106 0.25065 0.2506 RANDOM 34.733
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] 0.29 0.29 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.893 r_long_range_B_refined 8.535 r_dihedral_angle_2_deg 5.628 r_dihedral_angle_1_deg 5.452 r_scbond_it 5.243 r_mcangle_it 4.896 r_mcbond_it 3.572 r_angle_refined_deg 2.603 r_chiral_restr 0.174 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.893 r_long_range_B_refined 8.535 r_dihedral_angle_2_deg 5.628 r_dihedral_angle_1_deg 5.452 r_scbond_it 5.243 r_mcangle_it 4.896 r_mcbond_it 3.572 r_angle_refined_deg 2.603 r_chiral_restr 0.174 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3089 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing