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OMPD-domain of human UMPS in complex with UMP at 1.0 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, 1.6 - 1.8 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol
Cryo-protection: 100 mM Tris/HCl pH 8.0, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 1 M L-proline, 25 mM UMP
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.39 α = 90 b = 116.57 β = 90 c = 61.97 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 19.68 97.3 0.029 0.036 1 14.65 2.633 146396 13.035
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 1.05 98 0.678 0.854 0.643 1.61 2.503
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 19.68 139208 7188 97.26 0.1335 0.1328 0.1422 0.1471 0.1527 RANDOM 12.627
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] 0.11 -0.06 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.761 r_dihedral_angle_4_deg 14.908 r_dihedral_angle_3_deg 12.121 r_rigid_bond_restr 11.026 r_dihedral_angle_1_deg 6.943 r_angle_other_deg 2.233 r_angle_refined_deg 1.406 r_chiral_restr 0.077 r_bond_other_d 0.035 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.761 r_dihedral_angle_4_deg 14.908 r_dihedral_angle_3_deg 12.121 r_rigid_bond_restr 11.026 r_dihedral_angle_1_deg 6.943 r_angle_other_deg 2.233 r_angle_refined_deg 1.406 r_chiral_restr 0.077 r_bond_other_d 0.035 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1967 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction