4PVP

Crystal structure of malonate-bound human L-asparaginase protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZAKpdb entry 2ZAK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72932.2M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.459α = 90
b = 59.459β = 90
c = 298.9γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++MIRRORS2011-11-11MSINGLE 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
11.853094.70.04718.44828548285
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)
11.851.9669.50.2492.581.9

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 2ZAK1.8529.734534245342240693.60.1630.1610.204RANDOM23.09
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]
-3.91-3.917.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.905
r_dihedral_angle_3_deg15.418
r_dihedral_angle_4_deg13.64
r_dihedral_angle_1_deg5.956
r_scangle_it1.906
r_scbond_it1.255
r_angle_refined_deg1.21
r_mcangle_it0.858
r_mcbond_it0.488
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.905
r_dihedral_angle_3_deg15.418
r_dihedral_angle_4_deg13.64
r_dihedral_angle_1_deg5.956
r_scangle_it1.906
r_scbond_it1.255
r_angle_refined_deg1.21
r_mcangle_it0.858
r_mcbond_it0.488
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4309
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms9

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling