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Crystal structure of the genetically-encoded green calcium indicator NTnC in its calcium bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 286 0.1M Sodium acetate, 22.5% PEG3350, 10% PEG400, 5% DMSO.
Crystal Properties Matthews coefficient Solvent content 1.89 35.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.1 α = 90 b = 82.1 β = 90 c = 157.47 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 EIGER R 4M 2016-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.45 72.8 99.5 0.062 0.066 0.999 23.84 8.933 20432 -3 63.624
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.5 100 0.973 1.026 0.734 2.3 9.387
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4HVF 2.45 72.8 19409 1063 99.69 0.24259 0.23885 0.2389 0.30971 0.3097 RANDOM 61.224
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 22.257 r_dihedral_angle_3_deg 18 r_long_range_B_refined 11.749 r_mcangle_it 7.014 r_dihedral_angle_1_deg 6.945 r_scbond_it 4.9 r_mcbond_it 4.585 r_angle_refined_deg 1.86 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 22.257 r_dihedral_angle_3_deg 18 r_long_range_B_refined 11.749 r_mcangle_it 7.014 r_dihedral_angle_1_deg 6.945 r_scbond_it 4.9 r_mcbond_it 4.585 r_angle_refined_deg 1.86 r_chiral_restr 0.125 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_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 4112 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MoRDa phasing