4O0C

High resolution crystal structure of uncleaved human L-asparaginase protein


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
2.3447.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.213α = 90
b = 59.213β = 90
c = 297.793γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-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
11.530990.09213.28.19242692426
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)
11.51.5994.30.3482.864.114240

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 4GDV1.529.048442984429442595.190.154650.1520.20529RANDOM15.844
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]
-8.46-8.4616.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.621
r_dihedral_angle_3_deg14.282
r_dihedral_angle_4_deg12.289
r_sphericity_free9.051
r_dihedral_angle_1_deg6.562
r_sphericity_bonded4.73
r_rigid_bond_restr2.499
r_long_range_B_refined2.16
r_long_range_B_other2.122
r_scangle_other2.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.621
r_dihedral_angle_3_deg14.282
r_dihedral_angle_4_deg12.289
r_sphericity_free9.051
r_dihedral_angle_1_deg6.562
r_sphericity_bonded4.73
r_rigid_bond_restr2.499
r_long_range_B_refined2.16
r_long_range_B_other2.122
r_scangle_other2.004
r_mcangle_it1.894
r_mcangle_other1.894
r_scbond_it1.842
r_scbond_other1.841
r_mcbond_it1.751
r_mcbond_other1.751
r_angle_refined_deg1.559
r_angle_other_deg0.832
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4222
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms15

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling