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Structure of the Beta2_microglobulin involved in amyloidogenesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMG PDB ENTRY 1BMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6%PEG4000, 0.2M AMMONIUM SULPHATE, 0.1M NA-ACETEATE PH4.6
Crystal Properties Matthews coefficient Solvent content 2.91 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.49 α = 90 b = 100.864 β = 106.43 c = 83.743 γ = 90
Symmetry Space Group P 1 21 1
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.16 20 99.3 0.07 14.6 3.7 66127
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 2.16 2.24 99 0.32 3.1 3.6
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 SAD THROUGHOUT PDB ENTRY 1BMG 2.16 19.85 62741 3356 99.86 0.23962 0.23813 0.2531 0.26691 0.2748 RANDOM 60.626
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] -0.07 -0.03 0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.271 r_dihedral_angle_4_deg 21.78 r_dihedral_angle_3_deg 18.965 r_dihedral_angle_1_deg 9.84 r_scangle_it 5.596 r_scbond_it 3.678 r_angle_refined_deg 2.439 r_mcangle_it 2.269 r_mcbond_it 1.482 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.271 r_dihedral_angle_4_deg 21.78 r_dihedral_angle_3_deg 18.965 r_dihedral_angle_1_deg 9.84 r_scangle_it 5.596 r_scbond_it 3.678 r_angle_refined_deg 2.439 r_mcangle_it 2.269 r_mcbond_it 1.482 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.29 r_nbd_refined 0.282 r_xyhbond_nbd_refined 0.223 r_chiral_restr 0.187 r_symmetry_hbond_refined 0.17 r_bond_refined_d 0.028 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5930 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling PHASER phasing