3CQJ

Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (form B) complex with Zn2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CQH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7294PEG 4000, NaCl, pH 7.0, vapor diffusion, hanging drop, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.244.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.208α = 90
b = 132.596β = 90
c = 81.798γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2007-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID1.282APS31-ID

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
12.045097.60.07212.76.76760930.1
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)
12.052.1281.70.3873.45650

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 REPLACEMENTTHROUGHOUT3CQH2.045035543177997.850.1840.1830.213RANDOM32.213
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]
1.95-1.22-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.146
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg15.495
r_dihedral_angle_1_deg5.568
r_scangle_it2.683
r_scbond_it1.729
r_angle_refined_deg1.158
r_mcangle_it1.142
r_mcbond_it0.717
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.146
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg15.495
r_dihedral_angle_1_deg5.568
r_scangle_it2.683
r_scbond_it1.729
r_angle_refined_deg1.158
r_mcangle_it1.142
r_mcbond_it0.717
r_nbtor_refined0.299
r_symmetry_vdw_refined0.259
r_nbd_refined0.191
r_xyhbond_nbd_refined0.131
r_chiral_restr0.082
r_symmetry_hbond_refined0.06
r_metal_ion_refined0.053
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4375
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling