4OSY

STRUCTURE of FULLY-CLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GDTPDB ENTRY 4GDT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172932.2-2.5 M sodium Malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.736α = 90
b = 59.736β = 90
c = 301.527γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMARMOSAIC 225 mm CCD2012-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BMAPS22-BM

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
11.9151.7495.745006
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.912.0281.7

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 4GDT1.9129.722539842320227094.80.1840.1820.224RANDOM31.96
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]
-1.34-1.342.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_3_deg14.322
r_dihedral_angle_4_deg9.738
r_dihedral_angle_1_deg5.609
r_scangle_it1.625
r_scbond_it1.128
r_angle_refined_deg1.116
r_mcangle_it0.816
r_mcbond_it0.464
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_3_deg14.322
r_dihedral_angle_4_deg9.738
r_dihedral_angle_1_deg5.609
r_scangle_it1.625
r_scbond_it1.128
r_angle_refined_deg1.116
r_mcangle_it0.816
r_mcbond_it0.464
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4294
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
CrystalCleardata collection