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Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with 6-Methyl UMP
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 293 100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.375 α = 90 b = 116.687 β = 90 c = 62.027 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 2019-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.12 42.53 97.02 0.999 12.34 5.9 104066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.162 0.797
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.12 42.53 98954 5111 97.05 0.12413 0.12301 0.1238 0.14619 0.1461 RANDOM 15.372
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] 1.06 -0.37 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.146 r_dihedral_angle_4_deg 14.369 r_dihedral_angle_3_deg 12.716 r_dihedral_angle_1_deg 6.749 r_scangle_other 3.131 r_long_range_B_refined 3.039 r_rigid_bond_restr 2.928 r_long_range_B_other 2.835 r_scbond_it 2.578 r_scbond_other 2.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.146 r_dihedral_angle_4_deg 14.369 r_dihedral_angle_3_deg 12.716 r_dihedral_angle_1_deg 6.749 r_scangle_other 3.131 r_long_range_B_refined 3.039 r_rigid_bond_restr 2.928 r_long_range_B_other 2.835 r_scbond_it 2.578 r_scbond_other 2.522 r_angle_refined_deg 1.975 r_angle_other_deg 1.653 r_mcangle_other 1.505 r_mcangle_it 1.492 r_mcbond_it 1.399 r_mcbond_other 1.344 r_chiral_restr 0.113 r_gen_planes_refined 0.017 r_bond_refined_d 0.013 r_gen_planes_other 0.007 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1966 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing