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Resting state structure of the OMPD-domain of human UMPS variant (K314AcK) at 1.2 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Crystallization: 100 mM Tris/HCl pH 8.0, 1.9 - 2.1 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol
Cryo-protection: 100 mM Tris/HCl pH 8.0, 1.9 - 2.1 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 2 M L-proline
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.1 α = 90 b = 118.08 β = 90 c = 62.19 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 16M 2018-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97630 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 19.75 97.6 0.033 0.039 0.999 15.86 3.602 86563 22.067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.25 96.6 0.715 0.856 0.648 1.7 3.031
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QCD 1.2 19.75 82322 4241 97.59 0.1502 0.149 0.1582 0.1721 0.1796 RANDOM 21.805
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] 0.88 -0.05 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.727 r_dihedral_angle_3_deg 13.546 r_dihedral_angle_4_deg 12.683 r_rigid_bond_restr 8.592 r_dihedral_angle_1_deg 6.328 r_angle_other_deg 2.273 r_angle_refined_deg 1.497 r_chiral_restr 0.088 r_bond_other_d 0.035 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.727 r_dihedral_angle_3_deg 13.546 r_dihedral_angle_4_deg 12.683 r_rigid_bond_restr 8.592 r_dihedral_angle_1_deg 6.328 r_angle_other_deg 2.273 r_angle_refined_deg 1.497 r_chiral_restr 0.088 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1969 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction