8BI3

Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200W (crystal M200W#1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZAL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320-30% PEG4000, 10-15% PEG400, 0.2 M CaCl2 in 100 mM Tris-HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.4850.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.692α = 90
b = 70.844β = 90
c = 149.581γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97630PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.4574.7999.60.0850.0880.99916.113117826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.481.8281.9070.7971.612.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2ZAL1.45274.79117709106899.6440.1270.12680.162124.445
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]
1.0231.528-2.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.392
r_dihedral_angle_4_deg14.896
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg6.273
r_lrange_it4.879
r_lrange_other4.54
r_scangle_it4.206
r_scangle_other4.205
r_scbond_it3.493
r_scbond_other3.493
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.392
r_dihedral_angle_4_deg14.896
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg6.273
r_lrange_it4.879
r_lrange_other4.54
r_scangle_it4.206
r_scangle_other4.205
r_scbond_it3.493
r_scbond_other3.493
r_mcangle_other2.774
r_mcangle_it2.765
r_rigid_bond_restr2.253
r_mcbond_it2.181
r_mcbond_other2.165
r_angle_other_deg1.509
r_angle_refined_deg1.495
r_symmetry_nbd_refined0.262
r_nbd_other0.222
r_nbd_refined0.216
r_symmetry_xyhbond_nbd_refined0.177
r_symmetry_metal_ion_refined0.171
r_symmetry_nbd_other0.17
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.148
r_metal_ion_refined0.114
r_symmetry_nbtor_other0.085
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4267
Nucleic Acid Atoms
Solvent Atoms656
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing