4R8L

Crystal structure of the Asp-bound guinea pig L-asparaginase 1 catalytic domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M HEPES, 15% PEG 4000, 10 mM L-aspartic acid sodium salt monohydrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.21α = 90
b = 156β = 90
c = 158.82γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-GAPS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.41111.2998.758821
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.412.5596.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.4129.96155427294397.960.207270.20570.23612RANDOM45.378
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]
-0.4-0.631.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.826
r_dihedral_angle_4_deg19.025
r_dihedral_angle_3_deg13.807
r_long_range_B_refined9.416
r_long_range_B_other9.416
r_scangle_other7.238
r_dihedral_angle_1_deg5.867
r_mcangle_other5.696
r_mcangle_it5.317
r_scbond_other4.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.826
r_dihedral_angle_4_deg19.025
r_dihedral_angle_3_deg13.807
r_long_range_B_refined9.416
r_long_range_B_other9.416
r_scangle_other7.238
r_dihedral_angle_1_deg5.867
r_mcangle_other5.696
r_mcangle_it5.317
r_scbond_other4.925
r_scbond_it3.421
r_mcbond_it3.245
r_mcbond_other3.245
r_angle_refined_deg1.368
r_angle_other_deg0.99
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10854
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms36

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling