☰ Navigation Tabs
Crystal structure of beta-2-microglobulin D76E 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 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.63 α = 90 b = 28.871 β = 102.023 c = 67.508 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 0.9686 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 1.2 46.6 96.3 0.046 0.994 12.5 5.6 31346
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 1.2 1.22 0.306 0.828 3.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YXF 1.2 46.6 31345 1499 96.28 0.159 0.1582 0.1794 0.196 15.637
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] 0.415 0.341 -0.054 -0.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.001 r_dihedral_angle_4_deg 13.962 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 7.899 r_lrange_it 4.208 r_lrange_other 3.715 r_scangle_it 3.462 r_scangle_other 3.459 r_scbond_it 2.882 r_scbond_other 2.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.001 r_dihedral_angle_4_deg 13.962 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 7.899 r_lrange_it 4.208 r_lrange_other 3.715 r_scangle_it 3.462 r_scangle_other 3.459 r_scbond_it 2.882 r_scbond_other 2.881 r_rigid_bond_restr 2.079 r_mcangle_other 1.774 r_mcangle_it 1.769 r_angle_refined_deg 1.644 r_angle_other_deg 1.468 r_mcbond_it 1.273 r_mcbond_other 1.27 r_symmetry_nbd_refined 0.31 r_nbd_refined 0.258 r_nbd_other 0.228 r_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.215 r_symmetry_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.174 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 838 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Aimless data processing Coot model building PHASER phasing XDS data processing