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Crystal structure of the calcium indicator GCaMP6s-BrUS in calcium-bound 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 0.2 M Ammonium tartrate dibasic, pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.47 64.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.54 α = 90 b = 121.54 β = 90 c = 97.902 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 DECTRIS PILATUS 2M 2022-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.978 LNLS SIRIUS MANACA
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 2.65 47.52 99.3 0.182 0.197 0.072 0.994 9.1 7.2 21604
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 2.65 2.78 99.8 1.282 1.39 0.525 0.491 6.7
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 2.65 47.52 20498 1080 98.9 0.18334 0.18064 0.1807 0.23561 0.2357 RANDOM 54.331
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.683 r_long_range_B_refined 12.5 r_mcangle_it 8.193 r_scbond_it 7.543 r_dihedral_angle_2_deg 5.642 r_mcbond_it 5.464 r_dihedral_angle_1_deg 5.272 r_angle_refined_deg 2.949 r_chiral_restr 0.237 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.683 r_long_range_B_refined 12.5 r_mcangle_it 8.193 r_scbond_it 7.543 r_dihedral_angle_2_deg 5.642 r_mcbond_it 5.464 r_dihedral_angle_1_deg 5.272 r_angle_refined_deg 2.949 r_chiral_restr 0.237 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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 3117 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing