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Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K5W PDB ENTRY 1K5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 277 ammonium sulfate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.55 α = 90 b = 54.55 β = 90 c = 103.59 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.04 20 99 0.103 19.3 5.55 85544
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.04 1.06 96.6 0.416 1.62
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1K5W 1.04 19.5 85544 81211 4278 99 0.167 0.166 0.1664 0.184 0.1861 RANDOM 12.29
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] -0.48 -0.24 -0.48 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.204 r_sphericity_free 4.943 r_scangle_it 4.75 r_sphericity_bonded 4.285 r_scbond_it 3.02 r_mcangle_it 2.672 r_mcbond_it 1.752 r_angle_refined_deg 1.714 r_rigid_bond_restr 1.675 r_angle_other_deg 1.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.204 r_sphericity_free 4.943 r_scangle_it 4.75 r_sphericity_bonded 4.285 r_scbond_it 3.02 r_mcangle_it 2.672 r_mcbond_it 1.752 r_angle_refined_deg 1.714 r_rigid_bond_restr 1.675 r_angle_other_deg 1.433 r_symmetry_vdw_other 0.316 r_symmetry_vdw_refined 0.248 r_nbd_other 0.245 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.103 r_nbtor_other 0.089 r_metal_ion_refined 0.051 r_gen_planes_other 0.02 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1228 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing