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Crystallographic Identification of Sr2+ Coordination Site 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 VAPOR DIFFUSION, HANGING DROP 5 277 ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.644 α = 90 b = 54.644 β = 90 c = 103.317 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 0.9 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 1.18 20 95.5 0.048 31.1 10.9 56844
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 1.18 1.2 56.2 0.19 3.4
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 pdb entry 1K5W 1.18 20 53935 2861 95.47 0.15897 0.15818 0.1588 0.17373 0.1742 RANDOM 13.474
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] -0.49 -0.25 -0.49 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.39 r_sphericity_free 5.062 r_scangle_it 5.041 r_sphericity_bonded 3.955 r_scbond_it 3.201 r_mcangle_it 2.627 r_rigid_bond_restr 1.721 r_angle_refined_deg 1.71 r_mcbond_it 1.702 r_angle_other_deg 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.39 r_sphericity_free 5.062 r_scangle_it 5.041 r_sphericity_bonded 3.955 r_scbond_it 3.201 r_mcangle_it 2.627 r_rigid_bond_restr 1.721 r_angle_refined_deg 1.71 r_mcbond_it 1.702 r_angle_other_deg 0.912 r_symmetry_vdw_other 0.277 r_nbd_other 0.251 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.195 r_metal_ion_refined 0.192 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.099 r_symmetry_hbond_refined 0.092 r_nbtor_other 0.087 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 202 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing