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Complex between Vamp7 longin domain and fragment of delta-adaptin from AP3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX8 PDB ENTRY 2VX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 4 M NACL, 100 MM BICINE PH 9.0, 10 MM PRASEODYMIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.81 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.555 α = 90 b = 63.555 β = 90 c = 217.915 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 315 2011-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 64 100 0.31 7.3 13.1 11810
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 2.8 2.95 100 2.9 1.2 13.6
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 2VX8 2.8 61.01 11194 551 99.86 0.23164 0.23057 0.2306 0.25266 0.2624 RANDOM 60.83
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] 4.27 4.27 -8.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.888 r_dihedral_angle_3_deg 18.506 r_dihedral_angle_4_deg 17.412 r_dihedral_angle_1_deg 6.612 r_angle_refined_deg 1.566 r_angle_other_deg 1.189 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.888 r_dihedral_angle_3_deg 18.506 r_dihedral_angle_4_deg 17.412 r_dihedral_angle_1_deg 6.612 r_angle_refined_deg 1.566 r_angle_other_deg 1.189 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2439 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing