3EK5

Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EK6PDB ENTRY 3EK6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62980.1M Na Citrate, 19.5% PEG 3350, 0.05M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.634α = 90
b = 119.638β = 90
c = 125.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.97315NSRRCBL13C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.5686.3999.70.0630.0523.75.4556385539222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.562.6599.80.5040.33.35

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 3EK62.5627.352509281498.950.208580.206260.25157RANDOM55.136
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]
1.461.2-2.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.421
r_dihedral_angle_4_deg18.391
r_dihedral_angle_3_deg17.823
r_dihedral_angle_1_deg4.843
r_scangle_it1.766
r_mcangle_it1.755
r_angle_refined_deg1.382
r_mcbond_it1.041
r_scbond_it1.025
r_symmetry_vdw_refined0.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.421
r_dihedral_angle_4_deg18.391
r_dihedral_angle_3_deg17.823
r_dihedral_angle_1_deg4.843
r_scangle_it1.766
r_mcangle_it1.755
r_angle_refined_deg1.382
r_mcbond_it1.041
r_scbond_it1.025
r_symmetry_vdw_refined0.361
r_nbtor_refined0.33
r_nbd_refined0.268
r_symmetry_hbond_refined0.265
r_xyhbond_nbd_refined0.219
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10785
Nucleic Acid Atoms
Solvent Atoms507
Heterogen Atoms192

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling