4O0E

Crystal structure of the human L-asparaginase protein T186V 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
2.3647.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.378α = 90
b = 59.378β = 90
c = 298.322γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0782APS21-ID-D

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
11.713098.10.06214.415.286253762537
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)
11.711.8193.10.5591.653.3

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 4GDV1.7128.455740057400306694.880.175140.172470.2252RANDOM26.426
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]
0.410.41-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.008
r_dihedral_angle_3_deg17.986
r_dihedral_angle_4_deg9.639
r_dihedral_angle_1_deg6.97
r_long_range_B_refined3.174
r_long_range_B_other3.148
r_mcangle_it2.092
r_mcangle_other2.092
r_scangle_other1.993
r_angle_refined_deg1.603
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.008
r_dihedral_angle_3_deg17.986
r_dihedral_angle_4_deg9.639
r_dihedral_angle_1_deg6.97
r_long_range_B_refined3.174
r_long_range_B_other3.148
r_mcangle_it2.092
r_mcangle_other2.092
r_scangle_other1.993
r_angle_refined_deg1.603
r_mcbond_it1.498
r_mcbond_other1.498
r_scbond_it1.402
r_scbond_other1.402
r_angle_other_deg0.886
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4303
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms2

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling