6YWJ | pdb_00006ywj

Arabidopsis aspartate transcarbamoylase mutant F161A complex with UMP


X-RAY DIFFRACTION

Starting Model(s)

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

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) 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 coefficientSolvent content
2.7154.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.343α = 90
b = 104.343β = 90
c = 127.845γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

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
12.448.3041000.1940.9928.51030917
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)
12.42.491.2550.6292

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6YPO2.448.30430890153999.9770.1410.13830.140.19030.1842.89
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]
11.61711.617-23.234
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.096
r_dihedral_angle_4_deg19.435
r_dihedral_angle_3_deg17.261
r_lrange_it8.344
r_lrange_other8.343
r_dihedral_angle_1_deg7.95
r_scangle_it6.847
r_scangle_other6.846
r_mcangle_it5.774
r_mcangle_other5.774
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.096
r_dihedral_angle_4_deg19.435
r_dihedral_angle_3_deg17.261
r_lrange_it8.344
r_lrange_other8.343
r_dihedral_angle_1_deg7.95
r_scangle_it6.847
r_scangle_other6.846
r_mcangle_it5.774
r_mcangle_other5.774
r_scbond_it4.822
r_scbond_other4.822
r_mcbond_it4.353
r_mcbond_other4.351
r_angle_refined_deg1.784
r_angle_other_deg1.297
r_symmetry_nbd_refined0.247
r_symmetry_nbd_other0.205
r_nbd_refined0.203
r_nbd_other0.203
r_xyhbond_nbd_refined0.19
r_nbtor_refined0.167
r_symmetry_xyhbond_nbd_refined0.157
r_symmetry_xyhbond_nbd_other0.148
r_symmetry_nbtor_other0.091
r_chiral_restr0.072
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4884
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing