6WZ4

Complex of mutant (K173M) of Pseudomonas 7A Glutaminase-Asparaginase with L-Asp at pH 6. Covalent acyl-enzyme intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PGAPDB entry 4PGA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62938% w/v Tacsimate, pH 6.0, 20% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.034α = 90
b = 129.754β = 118.72
c = 81.409γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.5833.1498.70.0880.0510.9914.93.8191717
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6296.40.7250.4530.6542.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4PGA1.5833.14186557374797.720.1390.13870.1568RANDOM15.15
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]
0.050.020.08-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.652
r_dihedral_angle_4_deg12.792
r_dihedral_angle_3_deg12.459
r_dihedral_angle_1_deg6.412
r_angle_refined_deg1.804
r_angle_other_deg1.551
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.652
r_dihedral_angle_4_deg12.792
r_dihedral_angle_3_deg12.459
r_dihedral_angle_1_deg6.412
r_angle_refined_deg1.804
r_angle_other_deg1.551
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9928
Nucleic Acid Atoms
Solvent Atoms1125
Heterogen Atoms32

Software

Software
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing