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Beta2 microglobulin mutant H31Y displays hints for amyloid formations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDS PDB ENTRY 1LDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 300 PEG 4K 31%, glycerol 25%, ammonium acetate 0.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 3.88 68.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.195 α = 90 b = 150.166 β = 90 c = 93.671 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 100 M SINGLE WAVELENGTH 2 1 100
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.927 ELETTRA 5.2R 2 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
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 2.9 30 99.9 0.069 19.8 18871 16354
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1LDS 2.9 10 3 16354 15528 826 100 0.24084 0.23961 0.2514 0.31308 0.339 RANDOM 57.002
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] -1.33 4.75 -3.42
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 18.857 r_scbond_it 16.473 r_mcangle_it 16.232 r_mcbond_it 14.297 r_dihedral_angle_1_deg 10.376 r_angle_refined_deg 1.631 r_angle_other_deg 0.925 r_symmetry_hbond_refined 0.53 r_symmetry_vdw_other 0.412 r_nbd_refined 0.372
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 18.857 r_scbond_it 16.473 r_mcangle_it 16.232 r_mcbond_it 14.297 r_dihedral_angle_1_deg 10.376 r_angle_refined_deg 1.631 r_angle_other_deg 0.925 r_symmetry_hbond_refined 0.53 r_symmetry_vdw_other 0.412 r_nbd_refined 0.372 r_nbd_other 0.363 r_xyhbond_nbd_refined 0.318 r_symmetry_vdw_refined 0.276 r_chiral_restr 0.2 r_nbtor_other 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3356 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing