6WYZ

Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase (mutant K173M) in complex with D-Glu at pH 5.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1 M magnesium chloride, 50 mM Bis-Tris, pH 5.5, 20% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2244.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.282α = 90
b = 81.282β = 90
c = 176.703γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-11-03MSINGLE 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
11.739.6199.60.0880.030.99527.49.5142831
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)
11.71.7598.81.0920.4520.661.96.4

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 4PGA1.739.61137133372898.150.17250.17140.2148RANDOM17.784
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.47
r_dihedral_angle_4_deg17.01
r_dihedral_angle_3_deg14.72
r_dihedral_angle_1_deg6.865
r_angle_refined_deg2.233
r_angle_other_deg1.571
r_chiral_restr0.121
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.47
r_dihedral_angle_4_deg17.01
r_dihedral_angle_3_deg14.72
r_dihedral_angle_1_deg6.865
r_angle_refined_deg2.233
r_angle_other_deg1.571
r_chiral_restr0.121
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9494
Nucleic Acid Atoms
Solvent Atoms1274
Heterogen Atoms40

Software

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