6WYW

Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 4.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52930.1 M sodium acetate, pH 4.5, 25% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.728α = 90
b = 80.728β = 90
c = 176.401γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-08-09MSINGLE 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
12.1339.497.20.0610.0280.99527.35.771715
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)
12.132.1848.40.2670.1270.9415.65.1

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 4PGA2.1339.3868787278399.410.1440.14180.1982RANDOM25.673
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]
0.080.040.08-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.415
r_dihedral_angle_4_deg16.977
r_dihedral_angle_3_deg15.092
r_dihedral_angle_1_deg7.428
r_angle_refined_deg2.183
r_angle_other_deg1.562
r_chiral_restr0.113
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.415
r_dihedral_angle_4_deg16.977
r_dihedral_angle_3_deg15.092
r_dihedral_angle_1_deg7.428
r_angle_refined_deg2.183
r_angle_other_deg1.562
r_chiral_restr0.113
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9593
Nucleic Acid Atoms
Solvent Atoms870
Heterogen Atoms36

Software

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