5DNE

Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant K188M


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4R8L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M HEPES pH 7.0, 12-15% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
1.4917.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.91α = 90
b = 154.79β = 90
c = 157.31γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

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
12.393095.50.129.13.257320
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.392.5393.83.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4r8l2.393054025290494.820.195740.19360.23709RANDOM40.279
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]
0.250.55-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.469
r_dihedral_angle_4_deg18.474
r_dihedral_angle_3_deg14.419
r_long_range_B_refined7.177
r_long_range_B_other7.176
r_dihedral_angle_1_deg5.802
r_scangle_other4.935
r_mcangle_it4.22
r_mcangle_other4.22
r_scbond_it2.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.469
r_dihedral_angle_4_deg18.474
r_dihedral_angle_3_deg14.419
r_long_range_B_refined7.177
r_long_range_B_other7.176
r_dihedral_angle_1_deg5.802
r_scangle_other4.935
r_mcangle_it4.22
r_mcangle_other4.22
r_scbond_it2.982
r_scbond_other2.982
r_mcbond_it2.581
r_mcbond_other2.58
r_angle_refined_deg1.319
r_angle_other_deg0.946
r_chiral_restr0.065
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms10861
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing