4O0F

Crystal structure of the human L-asparaginase protein T219A mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GDVPDB entry 4GDV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72932.2-2.5 M sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3748.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.471α = 90
b = 59.471β = 90
c = 299.241γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++2012-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.923096.30.0611.782.94351643516
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.922.0487.60.3751.86

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 4GDV1.9229.594086340863221495.260.167190.164610.21481RANDOM26.434
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]
-3.2-3.26.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.013
r_dihedral_angle_3_deg19.315
r_dihedral_angle_4_deg18.048
r_dihedral_angle_1_deg7.805
r_long_range_B_refined3.815
r_long_range_B_other3.786
r_mcangle_it2.375
r_mcangle_other2.369
r_scangle_other2.243
r_angle_refined_deg1.741
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.013
r_dihedral_angle_3_deg19.315
r_dihedral_angle_4_deg18.048
r_dihedral_angle_1_deg7.805
r_long_range_B_refined3.815
r_long_range_B_other3.786
r_mcangle_it2.375
r_mcangle_other2.369
r_scangle_other2.243
r_angle_refined_deg1.741
r_mcbond_it1.695
r_mcbond_other1.688
r_scbond_it1.553
r_scbond_other1.548
r_angle_other_deg0.949
r_chiral_restr0.099
r_bond_refined_d0.012
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 Atoms4270
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms24

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling