1K2X

Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GAWPDB ENTRY 2GAW, polyalanine model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5292PEG 4000, PEG 400, magnesium chloride, Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.1643.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.296α = 90
b = 77.624β = 90
c = 148.152γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHToroidal mirror1999-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X311.0442EMBL/DESY, HAMBURGX31

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.65200.07516.85.67024970249-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6889.90.4762.55.5

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 2GAW, polyalanine model1.6519.56907769077106499.520.163490.162950.19836RANDOM10.18
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]
-0.090.51-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.832
r_dihedral_angle_1_deg3.992
r_scangle_it2.961
r_scbond_it1.763
r_angle_refined_deg1.411
r_angle_other_deg1.105
r_mcangle_it1.011
r_nbtor_other0.821
r_mcbond_it0.529
r_nbd_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.832
r_dihedral_angle_1_deg3.992
r_scangle_it2.961
r_scbond_it1.763
r_angle_refined_deg1.411
r_angle_other_deg1.105
r_mcangle_it1.011
r_nbtor_other0.821
r_mcbond_it0.529
r_nbd_refined0.3
r_symmetry_vdw_other0.223
r_nbd_other0.212
r_symmetry_hbond_refined0.187
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_other0.162
r_xyhbond_nbd_refined0.149
r_metal_ion_refined0.099
r_symmetry_hbond_other0.08
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4240
Nucleic Acid Atoms
Solvent Atoms575
Heterogen Atoms11

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement