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Crystal structure of dimeric S33C beta-2 microglobulin mutant in complex with Thioflavin (ThT) at 2.8 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S6C PDB ENTRY 3S6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 25% v/v PEG4000, 0.1 M sodium chloride, 5 mM thioflavin, 0.1 M HEPES sodium, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.45 64.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.038 α = 90 b = 80.038 β = 90 c = 177.7 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M 2014-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97088 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.8 177.7 100 0.059 21.4 9.6 16940 16940
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 1.139 2 10
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 (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 3S6C 2.8 69.31 16940 16036 862 99.91 0.17252 0.17075 0.1506 0.20649 0.1803 RANDOM 113.054
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] 26.34 26.34 -52.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.454 r_dihedral_angle_4_deg 28.387 r_dihedral_angle_3_deg 21.408 r_long_range_B_refined 13.135 r_long_range_B_other 13.133 r_scangle_other 10.519 r_dihedral_angle_1_deg 9.926 r_mcangle_it 9.81 r_mcangle_other 9.734 r_scbond_it 7.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.454 r_dihedral_angle_4_deg 28.387 r_dihedral_angle_3_deg 21.408 r_long_range_B_refined 13.135 r_long_range_B_other 13.133 r_scangle_other 10.519 r_dihedral_angle_1_deg 9.926 r_mcangle_it 9.81 r_mcangle_other 9.734 r_scbond_it 7.33 r_scbond_other 7.204 r_mcbond_it 6.823 r_mcbond_other 6.819 r_angle_other_deg 1.548 r_angle_refined_deg 1.453 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 3307 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 100
Software Software Software Name Purpose MxCuBE data collection BALBES phasing REFMAC refinement XDS data reduction SCALA data scaling