2W21

Crystal structure of the aminoacid kinase domain of the glutamate 5 kinase of Escherichia coli.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6LITHIUM SULFATE 1M, AMMONIUM SULFATE 0.5M, SODIUM SITRATE 0.1M PH 5.6
Crystal Properties
Matthews coefficientSolvent content
4.1570.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.358α = 90
b = 141.358β = 90
c = 78.373γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2008-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
12.95122.171000.115.615.4101732
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)
12.953.111000.441.715.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2J5T2.955096774901000.2090.2060.259RANDOM52.6
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]
-1.95-0.97-1.952.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.08
r_dihedral_angle_4_deg23.117
r_dihedral_angle_3_deg21.437
r_dihedral_angle_1_deg8.401
r_scangle_it3.873
r_scbond_it2.232
r_angle_refined_deg1.901
r_mcangle_it1.704
r_mcbond_it0.915
r_symmetry_hbond_refined0.491
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.08
r_dihedral_angle_4_deg23.117
r_dihedral_angle_3_deg21.437
r_dihedral_angle_1_deg8.401
r_scangle_it3.873
r_scbond_it2.232
r_angle_refined_deg1.901
r_mcangle_it1.704
r_mcbond_it0.915
r_symmetry_hbond_refined0.491
r_nbtor_refined0.314
r_nbd_refined0.251
r_symmetry_vdw_refined0.247
r_xyhbond_nbd_refined0.146
r_chiral_restr0.134
r_bond_refined_d0.018
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1788
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing