6YVB

Arabidopsis aspartate transcarbamoylase complex with carbamoyl phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YS6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293Protein 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 coefficientSolvent content
2.8356.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.268α = 90
b = 109.481β = 90
c = 212.042γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97910ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.82676.2781000.0510.99917.66.7212623
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)RedundancyNumber Unique Reflections (All)
11.8261.931.0580.704

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6YS61.82676.2782125131080099.9060.1740.1720.21337.606
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.031
r_dihedral_angle_4_deg18.377
r_dihedral_angle_3_deg15.809
r_lrange_it7.509
r_lrange_other7.482
r_dihedral_angle_1_deg6.896
r_scangle_it6.105
r_scangle_other6.105
r_scbond_it4.253
r_scbond_other4.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.031
r_dihedral_angle_4_deg18.377
r_dihedral_angle_3_deg15.809
r_lrange_it7.509
r_lrange_other7.482
r_dihedral_angle_1_deg6.896
r_scangle_it6.105
r_scangle_other6.105
r_scbond_it4.253
r_scbond_other4.253
r_mcangle_it4.212
r_mcangle_other4.212
r_mcbond_it3.303
r_mcbond_other3.303
r_angle_refined_deg1.692
r_angle_other_deg1.407
r_symmetry_nbd_refined0.225
r_nbd_refined0.199
r_nbd_other0.188
r_symmetry_nbd_other0.177
r_symmetry_xyhbond_nbd_refined0.165
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.156
r_chiral_restr0.083
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14733
Nucleic Acid Atoms
Solvent Atoms1334
Heterogen Atoms196

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing