4O0G

Crystal structure of the human L-asparaginase protein T219V 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
2.4349.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.439α = 90
b = 59.439β = 90
c = 306.794γ = 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
12.13097.90.09811.543.63495434954
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)
12.12.22960.5592.793.1

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 4GDV2.129.183297332973171297.10.168670.165150.2362RANDOM28.621
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]
-9.73-9.7319.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.805
r_dihedral_angle_3_deg20.258
r_dihedral_angle_4_deg15.253
r_dihedral_angle_1_deg7.234
r_long_range_B_refined4.164
r_long_range_B_other4.119
r_mcangle_it2.803
r_mcangle_other2.803
r_scangle_other2.623
r_mcbond_it1.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.805
r_dihedral_angle_3_deg20.258
r_dihedral_angle_4_deg15.253
r_dihedral_angle_1_deg7.234
r_long_range_B_refined4.164
r_long_range_B_other4.119
r_mcangle_it2.803
r_mcangle_other2.803
r_scangle_other2.623
r_mcbond_it1.959
r_mcbond_other1.956
r_scbond_it1.819
r_scbond_other1.819
r_angle_refined_deg1.766
r_angle_other_deg0.912
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4217
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms2

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling