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Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide Abeta(1-40)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MVK PDB ENTRY 4MVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 293 30 % (w/v) PEG 4000, 100 mM sodium acetate, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.71 27.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.95 α = 90 b = 58.93 β = 90 c = 61.23 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD mirrors 2010-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.7 42.46 99.9 0.055 20.3 6.9 20073 20073 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 99.9 0.245 0.245 3.1 6.9 2860
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4MVK 1.7 42.46 20073 20008 1020 99.66 0.1708 0.1687 0.1687 0.2123 0.2179 RANDOM 29.0034
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] 2.78 -1.27 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.264 r_dihedral_angle_4_deg 16.4 r_dihedral_angle_3_deg 16.002 r_dihedral_angle_1_deg 6.906 r_angle_refined_deg 1.96 r_chiral_restr 0.16 r_bond_refined_d 0.02 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection