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Crystal structure of the bright genetically encoded calcium indicator NCaMP7 based on mNeonGreen fluorescent protein
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 293 0.1M Sodium acetate pH 4.6; 0.2M Ammonium sulfate; 22% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.84 33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.9 α = 90 b = 65.7 β = 90 c = 93.02 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD 2019-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.79272 KURCHATOV SNC K4.4
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 1.75 37.99 100 0.158 0.165 0.998 14.54 11.355 38947 21.348
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 1.75 1.9 100 0.842 0.881 0.85 3.38 11.46
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 5MWC 1.75 37.99 37000 1947 99.95 0.1647 0.1632 0.1737 0.1933 0.1984 RANDOM 15.023
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 0.26 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.247 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 6.68 r_angle_refined_deg 1.812 r_angle_other_deg 1.53 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.247 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 6.68 r_angle_refined_deg 1.812 r_angle_other_deg 1.53 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3061 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 460
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction