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Crystal structure of beta-2-microglobulin D76A 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 2.09 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.665 α = 90 b = 28.799 β = 98.41 c = 62.289 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 44.41 97.7 0.014 0.999 32.4 6.3 30020
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 92.3 0.066 0.988 10.2 5.2
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 44.41 30020 1506 97.234 0.131 0.13 0.1586 0.1783 16.658
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] -0.22 0.12 0.418 -0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_4_deg 13.452 r_dihedral_angle_3_deg 12.06 r_rigid_bond_restr 10.286 r_dihedral_angle_1_deg 7.696 r_scbond_it 7.644 r_scbond_other 7.643 r_lrange_it 7.04 r_lrange_other 6.986 r_scangle_it 5.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.892 r_dihedral_angle_4_deg 13.452 r_dihedral_angle_3_deg 12.06 r_rigid_bond_restr 10.286 r_dihedral_angle_1_deg 7.696 r_scbond_it 7.644 r_scbond_other 7.643 r_lrange_it 7.04 r_lrange_other 6.986 r_scangle_it 5.289 r_scangle_other 5.289 r_angle_refined_deg 2.188 r_mcangle_other 2.145 r_mcangle_it 2.144 r_mcbond_it 1.592 r_mcbond_other 1.582 r_angle_other_deg 1.556 r_symmetry_xyhbond_nbd_refined 0.325 r_xyhbond_nbd_refined 0.237 r_nbd_refined 0.228 r_symmetry_nbd_other 0.209 r_symmetry_nbd_refined 0.188 r_xyhbond_nbd_other 0.185 r_nbtor_refined 0.18 r_chiral_restr 0.155 r_nbd_other 0.152 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 834 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data processing Coot model building PHASER phasing XDS data processing