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OMPD-domain of human UMPS in complex with the substrate OMP at 1.25 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 7.8 293 Crystallization: 100 mM Tris/HCl pH 8.0, 1.9 - 2.1 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol
Soaking: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP
Cryo-protection: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 50 mM OMP
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.766 α = 90 b = 116.906 β = 90 c = 62.047 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) 0.76530 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 1.1 58.52 100 0.071 0.077 0.999 13.53 6.737 114383 14.329
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 1.1 1.15 100 1.109 1.202 0.729 1.89 6.792
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 1.25 58.52 74471 3802 99.97 0.1174 0.1164 0.1173 0.1368 0.137 RANDOM 13.41
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] 0.79 -0.35 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.144 r_dihedral_angle_4_deg 17.486 r_dihedral_angle_3_deg 12.162 r_rigid_bond_restr 7.386 r_dihedral_angle_1_deg 6.795 r_angle_other_deg 2.26 r_angle_refined_deg 1.455 r_chiral_restr 0.08 r_bond_other_d 0.035 r_gen_planes_other 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.144 r_dihedral_angle_4_deg 17.486 r_dihedral_angle_3_deg 12.162 r_rigid_bond_restr 7.386 r_dihedral_angle_1_deg 6.795 r_angle_other_deg 2.26 r_angle_refined_deg 1.455 r_chiral_restr 0.08 r_bond_other_d 0.035 r_gen_planes_other 0.014 r_gen_planes_refined 0.011 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1962 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction