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Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 20% PEG3350
0.35 M Ammonium sulfate
0.1 M Tris (pH 8.5)
al's oil
Crystal Properties Matthews coefficient Solvent content 2.43 49.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.08 α = 90 b = 239.496 β = 114.92 c = 71.487 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 PIXEL DECTRIS PILATUS 6M 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.8 47.9 98.3 0.173 4.8 2.4 43944
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 96.2 2.4
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 5LOB 2.8 45.03 41690 2212 98.07 0.23944 0.23793 0.239 0.26857 0.2682 RANDOM 46.33
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] 6.32 -0.66 0.46 -6.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.15 r_dihedral_angle_3_deg 14.223 r_dihedral_angle_4_deg 11.536 r_dihedral_angle_1_deg 5.27 r_long_range_B_refined 2.146 r_long_range_B_other 2.146 r_angle_refined_deg 0.922 r_mcangle_it 0.903 r_mcangle_other 0.903 r_angle_other_deg 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.15 r_dihedral_angle_3_deg 14.223 r_dihedral_angle_4_deg 11.536 r_dihedral_angle_1_deg 5.27 r_long_range_B_refined 2.146 r_long_range_B_other 2.146 r_angle_refined_deg 0.922 r_mcangle_it 0.903 r_mcangle_other 0.903 r_angle_other_deg 0.798 r_scangle_other 0.54 r_mcbond_it 0.498 r_mcbond_other 0.498 r_scbond_it 0.287 r_scbond_other 0.287 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11138 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing XDS data reduction