☰ Navigation Tabs
Crystal structure of beta-2-microglobulin D76G 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 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.542 α = 90 b = 28.683 β = 98.466 c = 62.473 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 1.2 44.43 98.4 0.037 0.997 10.7 2.6 30235
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 98.4 0.219 0.911 2.9 2.6
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 1.2 44.43 30234 1517 98.188 0.141 0.1388 0.1515 0.174 0.1843 15.912
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] 0.025 -0.039 -1.222 1.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_dihedral_angle_4_deg 15.528 r_dihedral_angle_3_deg 10.658 r_rigid_bond_restr 9.586 r_dihedral_angle_1_deg 7.952 r_lrange_it 4.878 r_scangle_it 4.568 r_scangle_other 4.568 r_lrange_other 4.256 r_scbond_it 3.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.261 r_dihedral_angle_4_deg 15.528 r_dihedral_angle_3_deg 10.658 r_rigid_bond_restr 9.586 r_dihedral_angle_1_deg 7.952 r_lrange_it 4.878 r_scangle_it 4.568 r_scangle_other 4.568 r_lrange_other 4.256 r_scbond_it 3.825 r_scbond_other 3.824 r_mcangle_it 2.619 r_mcangle_other 2.617 r_angle_refined_deg 2.139 r_mcbond_other 1.951 r_mcbond_it 1.949 r_angle_other_deg 1.576 r_symmetry_nbd_refined 0.303 r_xyhbond_nbd_refined 0.285 r_symmetry_xyhbond_nbd_refined 0.263 r_nbd_other 0.241 r_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.173 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 833 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Coot model building PHASER phasing XDS data processing