2QLX

Crystal structure of rhamnose mutarotase RhaU of Rhizobium leguminosarum in complex with L-Rhamnose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QLWPDB entry 2QLW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62982M Sodium Formate, 0.1M Sodium Acetate pH 4.6, 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6653.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.652α = 90
b = 68.652β = 90
c = 100.719γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2006-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.853098.30.0934.22331723317
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)
11.851.9292.50.3223.72.82169

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2QLW228.51184171841794299.040.1380.1380.1350.188RANDOM16.591
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.064
r_dihedral_angle_4_deg18.664
r_dihedral_angle_3_deg14.36
r_dihedral_angle_1_deg5.452
r_scangle_it4.393
r_scbond_it3.093
r_angle_other_deg1.86
r_mcangle_it1.82
r_angle_refined_deg1.777
r_mcbond_it1.511
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.064
r_dihedral_angle_4_deg18.664
r_dihedral_angle_3_deg14.36
r_dihedral_angle_1_deg5.452
r_scangle_it4.393
r_scbond_it3.093
r_angle_other_deg1.86
r_mcangle_it1.82
r_angle_refined_deg1.777
r_mcbond_it1.511
r_mcbond_other0.341
r_symmetry_vdw_refined0.3
r_nbd_refined0.238
r_nbd_other0.21
r_symmetry_vdw_other0.192
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.184
r_symmetry_hbond_refined0.181
r_chiral_restr0.144
r_nbtor_other0.096
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1748
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms69

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
MOLREPphasing