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Crystal structure of human synaptotagmin 5 C2A domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 284 0.1M calcium acetate, 0.1M sodium acetate pH 5.6, 12.5%(w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.08 40.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.966 α = 90 b = 93.966 β = 90 c = 28.052 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU 2009-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54178
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 1.9 35 99.9 0.079 33.9 12.1 11445
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 1.9 1.93 99.1 0.425 5.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 30.76 10897 549 99.84 0.17259 0.17064 0.1705 0.21161 0.2097 RANDOM 19.668
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] -0.26 -0.13 -0.26 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_4_deg 11.634 r_dihedral_angle_1_deg 6.268 r_scangle_it 3.927 r_scbond_it 2.259 r_angle_refined_deg 1.256 r_mcangle_it 1.198 r_mcbond_it 0.609 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_4_deg 11.634 r_dihedral_angle_1_deg 6.268 r_scangle_it 3.927 r_scbond_it 2.259 r_angle_refined_deg 1.256 r_mcangle_it 1.198 r_mcbond_it 0.609 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1008 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing