☰ Navigation Tabs
Crystal structure of beta-2-microglobulin D76Y mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 100 nL mother liquor / 200 nL protein
15% Glycerol, 0.1 M NaAcetate pH 4.5-5.5, 28-32%PEG 4000, 0.2 M NH4Acetate
Crystal Properties Matthews coefficient Solvent content 1.9 35.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.706 α = 90 b = 27.691 β = 101.244 c = 64.521 γ = 90
Symmetry Space Group I 1 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 100 PIXEL DECTRIS PILATUS3 6M 2019-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.98 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 1.25 43.98 98 0.032 0.999 14.6 7 24565
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 81.4 0.927 0.448 0.9 5.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YXF 1.25 43.98 24562 1211 97.81 0.181 0.1785 0.1788 0.2272 0.2279 19.957
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] 0.343 0.59 -0.637 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.516 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 13.699 r_dihedral_angle_1_deg 8.703 r_lrange_it 4.209 r_lrange_other 3.672 r_scangle_it 2.852 r_scangle_other 2.848 r_scbond_it 2.428 r_scbond_other 2.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.516 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 13.699 r_dihedral_angle_1_deg 8.703 r_lrange_it 4.209 r_lrange_other 3.672 r_scangle_it 2.852 r_scangle_other 2.848 r_scbond_it 2.428 r_scbond_other 2.417 r_mcangle_it 2.414 r_mcangle_other 2.413 r_angle_refined_deg 2.263 r_rigid_bond_restr 2.194 r_mcbond_it 1.905 r_mcbond_other 1.904 r_angle_other_deg 1.757 r_symmetry_nbd_refined 0.28 r_nbd_other 0.255 r_symmetry_nbd_other 0.226 r_symmetry_xyhbond_nbd_refined 0.224 r_xyhbond_nbd_refined 0.216 r_nbtor_refined 0.207 r_nbd_refined 0.196 r_symmetry_nbtor_other 0.111 r_chiral_restr 0.084 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 841 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data processing Coot model building PHASER phasing XDS data processing