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Crystal structure of beta-2-microglobulin D76K 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 1.81 31.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.43 α = 90 b = 27.721 β = 96.692 c = 60.048 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 2M 2018-09-13 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 1.24 41.24 97.2 0.034 0.999 13.2 3.7 23336
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 1.24 1.26 72.4 0.405 0.691 1.8 2.7
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 1.242 41.24 23332 1147 97.132 0.194 0.1922 0.2002 0.2301 0.234 12.336
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] 0.818 -1.21 -0.666 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.266 r_dihedral_angle_4_deg 20.126 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_1_deg 9.422 r_rigid_bond_restr 5.69 r_lrange_it 3.257 r_lrange_other 2.699 r_angle_refined_deg 2.418 r_scangle_it 2.128 r_scangle_other 2.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.266 r_dihedral_angle_4_deg 20.126 r_dihedral_angle_3_deg 12.675 r_dihedral_angle_1_deg 9.422 r_rigid_bond_restr 5.69 r_lrange_it 3.257 r_lrange_other 2.699 r_angle_refined_deg 2.418 r_scangle_it 2.128 r_scangle_other 2.123 r_scbond_it 2.041 r_scbond_other 2.03 r_angle_other_deg 1.982 r_mcangle_other 1.79 r_mcangle_it 1.787 r_mcbond_it 1.616 r_mcbond_other 1.503 r_symmetry_xyhbond_nbd_refined 0.289 r_nbd_other 0.252 r_symmetry_nbd_other 0.236 r_nbtor_refined 0.218 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.186 r_symmetry_nbd_refined 0.181 r_symmetry_nbtor_other 0.114 r_chiral_restr 0.11 r_bond_refined_d 0.033 r_bond_other_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 829 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data processing Coot model building PHASER phasing XDS data processing