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Arabidopsis aspartate transcarbamoylase mutant F161A complex with UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP) and with 5 mM UMP.
Crystallization solution: 18-22 % PEG3350, 0.1 M Na2SO4 and 0.1 M bis-tris pH 6.5
Crystals were cryo-protected by soaking in a solution containing the mother liquor supplemented with 20% glycerol and the 5 mM UMP.
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.343 α = 90 b = 104.343 β = 90 c = 127.845 γ = 120
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 PILATUS 6M 2019-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 48.304 100 0.194 0.992 8.5 10 30917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 1.255 0.629 2
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6YPO 2.4 48.304 30890 1539 99.977 0.141 0.1383 0.1903 0.1849 42.89
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] 11.617 11.617 -23.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.096 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_3_deg 17.261 r_lrange_it 8.344 r_lrange_other 8.343 r_dihedral_angle_1_deg 7.95 r_scangle_it 6.847 r_scangle_other 6.846 r_mcangle_it 5.774 r_mcangle_other 5.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.096 r_dihedral_angle_4_deg 19.435 r_dihedral_angle_3_deg 17.261 r_lrange_it 8.344 r_lrange_other 8.343 r_dihedral_angle_1_deg 7.95 r_scangle_it 6.847 r_scangle_other 6.846 r_mcangle_it 5.774 r_mcangle_other 5.774 r_scbond_it 4.822 r_scbond_other 4.822 r_mcbond_it 4.353 r_mcbond_other 4.351 r_angle_refined_deg 1.784 r_angle_other_deg 1.297 r_symmetry_nbd_refined 0.247 r_symmetry_nbd_other 0.205 r_nbd_refined 0.203 r_nbd_other 0.203 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.148 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4884 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing