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Human UMP Synthase (C-terminal Domain- Orotidine 5'-Monophosphate Decarboxylase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 2.28M Ammonium sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.571 α = 90 b = 59.37 β = 114.3 c = 69.863 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD BRUKER SMART 6000 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.88 63.67 97.8 0.1414 0.171 4.29 1.84 11598 11348
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.88 2.9 28.9 0.4 0.5454 2.04 0.49 232
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1DQW 2.88 63.63 11029 10398 522 94.28 0.26179 0.26179 0.25946 0.2577 0.30737 0.2968 RANDOM 10.041
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] 2.07 2.38 -1.84 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.917 r_dihedral_angle_3_deg 19.021 r_dihedral_angle_4_deg 18.059 r_dihedral_angle_1_deg 8.528 r_scangle_it 3.588 r_scbond_it 2.12 r_angle_refined_deg 1.993 r_mcangle_it 1.326 r_mcbond_it 0.892 r_symmetry_hbond_refined 0.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.917 r_dihedral_angle_3_deg 19.021 r_dihedral_angle_4_deg 18.059 r_dihedral_angle_1_deg 8.528 r_scangle_it 3.588 r_scbond_it 2.12 r_angle_refined_deg 1.993 r_mcangle_it 1.326 r_mcbond_it 0.892 r_symmetry_hbond_refined 0.356 r_nbtor_refined 0.343 r_symmetry_vdw_refined 0.337 r_chiral_restr 0.32 r_nbd_refined 0.274 r_xyhbond_nbd_refined 0.171 r_bond_refined_d 0.025 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3916 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection SAINT data reduction SADABS data scaling PHASER phasing