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Crystal structure of beta-2-microglobulin D76Q 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 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.342 α = 90 b = 28.802 β = 102.01 c = 67.564 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 1.51 46.4 95.6 0.085 0.982 7.9 2.7 15590
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 1.51 1.54 95.7 0.716 0.354 3.6 2.3
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 1.51 46.4 15588 802 95.345 0.224 0.2214 0.2295 0.2662 0.2769 14.384
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] -0.345 -0.358 0.325 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.644 r_dihedral_angle_4_deg 22.818 r_dihedral_angle_3_deg 15.129 r_dihedral_angle_1_deg 8.11 r_lrange_it 6.076 r_lrange_other 5.878 r_scangle_it 3.628 r_scangle_other 3.621 r_scbond_it 2.266 r_scbond_other 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.644 r_dihedral_angle_4_deg 22.818 r_dihedral_angle_3_deg 15.129 r_dihedral_angle_1_deg 8.11 r_lrange_it 6.076 r_lrange_other 5.878 r_scangle_it 3.628 r_scangle_other 3.621 r_scbond_it 2.266 r_scbond_other 2.266 r_mcangle_other 2.222 r_mcangle_it 2.216 r_angle_refined_deg 1.706 r_mcbond_it 1.43 r_mcbond_other 1.374 r_angle_other_deg 1.355 r_symmetry_xyhbond_nbd_refined 0.342 r_xyhbond_nbd_refined 0.268 r_symmetry_nbd_refined 0.233 r_nbd_other 0.212 r_symmetry_nbd_other 0.197 r_nbd_refined 0.189 r_nbtor_refined 0.171 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 138 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data processing Coot model building PHASER phasing XDS data processing