2UYT

Structure of L-rhamnulose kinase in complex with ADP and beta-L- rhamnulose.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CGLPDB ENTRY 2CGL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
117% (W/V) PEG 8000, 0.12 M LICL, 20 MM ADP, 20 MM L-RHAMNULOSE-1-PHOSPHATE
Crystal Properties
Matthews coefficientSolvent content
1.935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.043α = 90
b = 51.093β = 90
c = 158.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS 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
11.558098.60.0523.26.9604014.7
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)
11.551.6289.40.374.75.5

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 2CGL1.5579.3157380302198.60.1810.1790.209RANDOM14.5
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]
0.11-0.230.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.628
r_dihedral_angle_4_deg21.145
r_dihedral_angle_3_deg14.727
r_dihedral_angle_1_deg5.42
r_scangle_it2.513
r_scbond_it1.657
r_angle_refined_deg1.342
r_mcangle_it1.032
r_mcbond_it0.652
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.628
r_dihedral_angle_4_deg21.145
r_dihedral_angle_3_deg14.727
r_dihedral_angle_1_deg5.42
r_scangle_it2.513
r_scbond_it1.657
r_angle_refined_deg1.342
r_mcangle_it1.032
r_mcbond_it0.652
r_nbtor_refined0.303
r_symmetry_vdw_refined0.207
r_nbd_refined0.198
r_symmetry_hbond_refined0.151
r_chiral_restr0.082
r_bond_refined_d0.01
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_refined
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 Atoms322
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing