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Arabidopsis aspartate transcarbamoylase complex with carbamoyl phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YS6
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), with 10 mM carbamoyl phosphate. Crystallization solution: 25% PEG3350, 0.2 M Li2SO4 and 0.1 M bis-tris pH 5.5. Cryo-conditions achieved by increasing glycerol concentration up to 20% in presence of carbamoyl phosphate.
Crystal Properties Matthews coefficient Solvent content 2.83 56.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.268 α = 90 b = 109.481 β = 90 c = 212.042 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2019-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97910 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 1.826 76.278 100 0.051 0.999 17.6 6.7 212623
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 1.826 1.93 1.058 0.704
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6YS6 1.826 76.278 212513 10800 99.906 0.174 0.172 0.1801 0.213 0.2206 37.606
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] 1.068 -0.039 -1.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.031 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 15.809 r_lrange_it 7.509 r_lrange_other 7.482 r_dihedral_angle_1_deg 6.896 r_scangle_it 6.105 r_scangle_other 6.105 r_scbond_it 4.253 r_scbond_other 4.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.031 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 15.809 r_lrange_it 7.509 r_lrange_other 7.482 r_dihedral_angle_1_deg 6.896 r_scangle_it 6.105 r_scangle_other 6.105 r_scbond_it 4.253 r_scbond_other 4.253 r_mcangle_it 4.212 r_mcangle_other 4.212 r_mcbond_it 3.303 r_mcbond_other 3.303 r_angle_refined_deg 1.692 r_angle_other_deg 1.407 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.199 r_nbd_other 0.188 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14733 Nucleic Acid Atoms Solvent Atoms 1334 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing