4PVQ

Crystal structure of sulfate-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
1VAPOR DIFFUSION, HANGING DROP5.272930.2 M AMMONIUM IODIDE, 2.2 M AMMONIUM SULFATE, PH 5.27, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.22α = 90
b = 59.22β = 90
c = 298.5γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++MIRRORS2012-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.133079.40.06712.82628526285
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)
12.132.2553.50.3252.892.06

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 4GDT2.13302443724437133377.80.1690.1660.222RANDOM27.2
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]
-0.18-0.180.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.177
r_dihedral_angle_3_deg17.438
r_dihedral_angle_4_deg14.413
r_dihedral_angle_1_deg6.19
r_scangle_it2.033
r_scbond_it1.584
r_angle_refined_deg1.298
r_mcangle_it0.874
r_mcbond_it0.488
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.177
r_dihedral_angle_3_deg17.438
r_dihedral_angle_4_deg14.413
r_dihedral_angle_1_deg6.19
r_scangle_it2.033
r_scbond_it1.584
r_angle_refined_deg1.298
r_mcangle_it0.874
r_mcbond_it0.488
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4257
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms71

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling