2CGJ

Crystal Structure of L-rhamnulose kinase from Escherichia coli in complex with L-fructose and ADP.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
117% PEG 8000, 120 MM LICL
Crystal Properties
Matthews coefficientSolvent content
1.935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.729α = 90
b = 51.305β = 90
c = 159.263γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-09-06MSINGLE WAVELENGTH
21x-ray
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1
2SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
12.264999.20.077.47.620321
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)
12.262.3494.10.553.74.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.2649.2119305101799.20.2080.2060.25RANDOM56.79
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]
2.29-0.84-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.182
r_dihedral_angle_3_deg15.731
r_dihedral_angle_4_deg14.719
r_dihedral_angle_1_deg4.947
r_scangle_it1.034
r_angle_refined_deg1.027
r_scbond_it0.63
r_mcangle_it0.568
r_mcbond_it0.325
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.182
r_dihedral_angle_3_deg15.731
r_dihedral_angle_4_deg14.719
r_dihedral_angle_1_deg4.947
r_scangle_it1.034
r_angle_refined_deg1.027
r_scbond_it0.63
r_mcangle_it0.568
r_mcbond_it0.325
r_nbtor_refined0.294
r_nbd_refined0.174
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.127
r_xyhbond_nbd_refined0.118
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.002
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 Atoms3707
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing