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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 3F00 PDB entry 3F00
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
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.088 α = 90 b = 38.561 β = 97.35 c = 44.267 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 SBC-3 2008-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.379 APS 19-ID
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 1.7 50 99.4 0.05 54.378 5.3 15627
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) 1.7 1.73 97.4 0.164 4.5 1484
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 3F00 1.7 28.98 15625 779 99.57 0.195 0.193 0.1855 0.229 0.2163 RANDOM 20.386
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 33.468 r_dihedral_angle_3_deg 9.531 r_dihedral_angle_4_deg 5.364 r_sphericity_free 4.056 r_dihedral_angle_1_deg 3.903 r_sphericity_bonded 3.864 r_mcangle_it 2.332 r_scangle_it 1.955 r_mcbond_it 1.571 r_scbond_it 1.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.468 r_dihedral_angle_3_deg 9.531 r_dihedral_angle_4_deg 5.364 r_sphericity_free 4.056 r_dihedral_angle_1_deg 3.903 r_sphericity_bonded 3.864 r_mcangle_it 2.332 r_scangle_it 1.955 r_mcbond_it 1.571 r_scbond_it 1.382 r_angle_refined_deg 1.351 r_rigid_bond_restr 1.323 r_nbtor_refined 0.32 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.236 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.198 r_metal_ion_refined 0.194 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_symmetry_metal_ion_refined 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1150 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling