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Structure of a single domain camelid antibody fragment in complex with a C-terminal peptide of alpha-synuclein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HCV PDB ENTRY 1HCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 25% PEG6000, 100 MM HEPES PH 7.5, 100 MM LICL
Crystal Properties Matthews coefficient Solvent content 2.01 38.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.17 α = 90 b = 63.12 β = 90 c = 62.87 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 IMAGE PLATE MAR555 FLAT PANEL M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.62 30 99.9 0.12 23.3 14.3 15482 18.126
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 1.62 1.71 99.9 0.54 4.3 14.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HCV 1.62 43.56 14361 1101 99.93 0.1596 0.15634 0.20258 0.2054 RANDOM 17.91
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] -0.47 -0.19 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.154 r_dihedral_angle_4_deg 24.031 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_1_deg 7.031 r_scangle_it 5.539 r_scbond_it 3.561 r_mcangle_it 2.481 r_angle_refined_deg 1.693 r_mcbond_it 1.531 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.154 r_dihedral_angle_4_deg 24.031 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_1_deg 7.031 r_scangle_it 5.539 r_scbond_it 3.561 r_mcangle_it 2.481 r_angle_refined_deg 1.693 r_mcbond_it 1.531 r_chiral_restr 0.147 r_bond_refined_d 0.018 r_gen_planes_refined 0.015 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 993 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing