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OMPD-domain of human UMPS in complex with 6-Aza-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 6-Aza-UMP
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.67 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) 0.72930 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 97.7 0.045 0.052 1 14.65 3.851 147538 11.851
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 98.8 0.786 0.909 0.615 1.78 3.813
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 140278 7260 97.65 0.1228 0.122 0.1226 0.1376 0.138 RANDOM 11.243
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] 0.24 -0.15 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.243 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 12.627 r_rigid_bond_restr 8.744 r_dihedral_angle_1_deg 6.515 r_angle_other_deg 2.284 r_angle_refined_deg 1.675 r_chiral_restr 0.095 r_bond_other_d 0.034 r_gen_planes_other 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.243 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 12.627 r_rigid_bond_restr 8.744 r_dihedral_angle_1_deg 6.515 r_angle_other_deg 2.284 r_angle_refined_deg 1.675 r_chiral_restr 0.095 r_bond_other_d 0.034 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1959 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction