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Arabidopsis aspartate transcarbamoylase bound to UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2 % glycerol and 0.2 mM tris(2-carboxyethyl) phosphine (TCEP).
Crystallization reservoir: 22 % PEG 3350, 0.1 M sodium sulfate, 0.1 M bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.541 α = 90 b = 104.541 β = 90 c = 127.79 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 110 PIXEL DECTRIS PILATUS3 S 6M 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 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 1.67 90.54 99.38 0.1046 0.997 12.74 10.3 91035 28.26
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 1.67 1.73 99.99 1.396 0.601 1.64 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5G1N 1.67 90.54 21.86 91035 4638 99.38 0.1518 0.1494 0.1679 0.1605 34.15
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.2207 f_angle_d 0.6425 f_chiral_restr 0.0438 f_bond_d 0.005 f_plane_restr 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4896 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement EDNA data collection autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing