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Crystal structure of beta-2-microglobulin D76S 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 2.07 40.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.339 α = 90 b = 28.795 β = 96.93 c = 63.004 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 ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
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 1.15 38.2 98.6 0.031 0.998 10.7 2.8 33548
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 1.15 1.17 98.4 0.916 0.504 0.8 2.8
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 1.15 38.2 33547 1675 98.526 0.15 0.1479 0.1481 0.1823 0.182 20.47
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] 0.579 1.201 -1.38 0.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.846 r_dihedral_angle_4_deg 22.879 r_dihedral_angle_3_deg 11.276 r_rigid_bond_restr 9.394 r_dihedral_angle_1_deg 7.584 r_lrange_it 5.2 r_scangle_it 5.184 r_scangle_other 5.18 r_lrange_other 4.61 r_scbond_it 4.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.846 r_dihedral_angle_4_deg 22.879 r_dihedral_angle_3_deg 11.276 r_rigid_bond_restr 9.394 r_dihedral_angle_1_deg 7.584 r_lrange_it 5.2 r_scangle_it 5.184 r_scangle_other 5.18 r_lrange_other 4.61 r_scbond_it 4.542 r_scbond_other 4.537 r_mcbond_it 3.26 r_mcangle_other 3.02 r_mcangle_it 2.966 r_mcbond_other 2.1 r_angle_refined_deg 1.893 r_angle_other_deg 1.534 r_symmetry_xyhbond_nbd_refined 0.276 r_nbd_other 0.256 r_symmetry_nbd_refined 0.236 r_xyhbond_nbd_refined 0.235 r_symmetry_nbd_other 0.196 r_nbd_refined 0.19 r_symmetry_xyhbond_nbd_other 0.185 r_nbtor_refined 0.177 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.085 r_xyhbond_nbd_other 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 818 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data processing Coot model building PHASER phasing XDS data processing