6V2B

Complex of double mutant (T89V,K162T) of E. coli L-asparaginase II with L-Asn


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ECA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298Crystals grown at 0.17 M sodium citrate (pH 6) and 17-18% (w/v) PEG3350. Soaked for 1-2 minutes (empirically determined for each crystal) in equivalent solution with 0.025% (w/v) glutaraldehyde. Finally transferred and soaked for 10-20 sec in solution containing 40% (w/v) PEG3350, 5 mM L-Asn, and 0.17 M sodium citrate (pH 5.5)
Crystal Properties
Matthews coefficientSolvent content
2.0840.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.224α = 90
b = 62.578β = 117.67
c = 140.886γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2017-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.054095.70.0470.0570.03312.52.870596
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.0994.60.5120.6320.3640.7062.5

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 REPLACEMENTTHROUGHOUT3eca2.0526.5565221339693.280.15470.15220.2013RANDOM28.11
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]
0.090.01-0.20.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.397
r_dihedral_angle_4_deg18.678
r_dihedral_angle_3_deg15.496
r_dihedral_angle_1_deg7.376
r_angle_refined_deg1.915
r_angle_other_deg1.472
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.397
r_dihedral_angle_4_deg18.678
r_dihedral_angle_3_deg15.496
r_dihedral_angle_1_deg7.376
r_angle_refined_deg1.915
r_angle_other_deg1.472
r_chiral_restr0.091
r_bond_refined_d0.015
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 Atoms9619
Nucleic Acid Atoms
Solvent Atoms679
Heterogen Atoms75

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing