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Crystal Structure of Synaptotagmin I C2A domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.0M Li2SO4, 100mM Tris, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.99 α = 90 b = 38.67 β = 97.26 c = 44.33 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 2005-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 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 1.35 50 97.4 0.047 35.117 6.4 30486
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) 1.35 1.4 86.2 0.154 5 2688
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.35 28.5 30467 1539 97.29 0.196 0.194 0.224 0.2489 RANDOM 19.814
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 32.108 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_3_deg 8.625 r_dihedral_angle_1_deg 3.927 r_sphericity_bonded 1.994 r_mcangle_it 1.717 r_sphericity_free 1.595 r_scangle_it 1.589 r_angle_refined_deg 1.179 r_mcbond_it 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_3_deg 8.625 r_dihedral_angle_1_deg 3.927 r_sphericity_bonded 1.994 r_mcangle_it 1.717 r_sphericity_free 1.595 r_scangle_it 1.589 r_angle_refined_deg 1.179 r_mcbond_it 1.135 r_scbond_it 1.09 r_rigid_bond_restr 0.929 r_nbtor_refined 0.319 r_nbd_refined 0.277 r_symmetry_vdw_refined 0.245 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1112 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling