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1.25 Angstrom crystal structure of Ca/CaM A102V:RyR2 peptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Sodium acetate trihydrate pH 4.0, 25% w/v Polyethylene glycol 1,500
Crystal Properties Matthews coefficient Solvent content 1.87 34.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.11 α = 90 b = 41.8 β = 90 c = 86.02 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 PIXEL DECTRIS PILATUS3 6M 2018-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
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 1.23 41.8 98.37 0.038 0.042 0.017 0.999 18.4 5.6 42088 16.8
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 1.23 1.25 83.25 0.789 0.971 0.553 0.473 1.2 2.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6XXF 1.25 37.624 40399 2015 98.952 0.144 0.1417 0.1419 0.1892 0.1897 23.636
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] -1.27 3.864 -2.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.718 r_dihedral_angle_4_deg 15.197 r_dihedral_angle_3_deg 14.639 r_rigid_bond_restr 13.187 r_scangle_it 6.194 r_scangle_other 6.194 r_lrange_it 6.09 r_lrange_other 5.767 r_scbond_it 5.479 r_scbond_other 5.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.718 r_dihedral_angle_4_deg 15.197 r_dihedral_angle_3_deg 14.639 r_rigid_bond_restr 13.187 r_scangle_it 6.194 r_scangle_other 6.194 r_lrange_it 6.09 r_lrange_other 5.767 r_scbond_it 5.479 r_scbond_other 5.479 r_dihedral_angle_1_deg 5.287 r_mcangle_it 3.67 r_mcangle_other 3.669 r_mcbond_it 3.339 r_mcbond_other 3.337 r_angle_refined_deg 2.065 r_angle_other_deg 1.681 r_nbd_other 0.244 r_nbd_refined 0.242 r_symmetry_xyhbond_nbd_other 0.207 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.172 r_symmetry_nbd_refined 0.15 r_metal_ion_refined 0.126 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1327 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing