5DND

Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A


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
1.4917.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.86α = 90
b = 154.78β = 90
c = 157.28γ = 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
12.293098.50.1213.385.266847
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.292.4395.25.1

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 REPLACEMENTTHROUGHOUT4r8l2.293062995331697.730.209680.2080.24229RANDOM37.695
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]
0.23-0.21-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.134
r_dihedral_angle_4_deg18.439
r_dihedral_angle_3_deg14.075
r_long_range_B_refined6.927
r_long_range_B_other6.927
r_dihedral_angle_1_deg5.566
r_scangle_other4.729
r_mcangle_it4.011
r_mcangle_other4.01
r_scbond_it2.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.134
r_dihedral_angle_4_deg18.439
r_dihedral_angle_3_deg14.075
r_long_range_B_refined6.927
r_long_range_B_other6.927
r_dihedral_angle_1_deg5.566
r_scangle_other4.729
r_mcangle_it4.011
r_mcangle_other4.01
r_scbond_it2.842
r_scbond_other2.842
r_mcbond_it2.418
r_mcbond_other2.418
r_angle_refined_deg1.32
r_angle_other_deg0.94
r_chiral_restr0.066
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 Atoms10851
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building