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Crystal Structure of Synaptotagmin I C2A domain with Cu(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RSY PDB entry 1RSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.647 α = 90 b = 38.363 β = 98.37 c = 44.016 γ = 90
Symmetry Space Group P 1 21 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 CCD 2005-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98268 APS 19-BM
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 1.36 100 95.6 0.165 15.786 4.1 28585
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) 1.36 1.41 73.2 0.514 2.2 2177
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 1RSY 1.36 20.6 28466 1414 99.28 0.203 0.201 0.196 0.244 0.2343 RANDOM 17.97
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.043 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_4_deg 5.777 r_dihedral_angle_1_deg 3.875 r_sphericity_bonded 3.782 r_sphericity_free 3.142 r_mcangle_it 2.099 r_scangle_it 1.851 r_mcbond_it 1.397 r_scbond_it 1.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.043 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_4_deg 5.777 r_dihedral_angle_1_deg 3.875 r_sphericity_bonded 3.782 r_sphericity_free 3.142 r_mcangle_it 2.099 r_scangle_it 1.851 r_mcbond_it 1.397 r_scbond_it 1.294 r_angle_refined_deg 1.253 r_rigid_bond_restr 1.159 r_nbtor_refined 0.324 r_nbd_refined 0.284 r_symmetry_vdw_refined 0.257 r_xyhbond_nbd_refined 0.227 r_symmetry_hbond_refined 0.195 r_symmetry_metal_ion_refined 0.12 r_metal_ion_refined 0.119 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1166 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing