3CU2

Crystal structure of ribulose-5-phosphate 3-epimerase (YP_718263.1) from Haemophilus somnus 129PT at 1.91 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.17277NANODROP, 16.0% PEG 8000, 0.167M Calcium acetate, 0.1M MES pH 6.17, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7154.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.01α = 90
b = 85.01β = 90
c = 140.16γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-02-04MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837, 0.97922, 0.97840SSRLBL11-1

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
11.9128.91699.80.127.7246203-319.326
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)
11.911.9899.80.7641.4

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 DIFFRACTIONMADTHROUGHOUT1.9128.91646156233599.830.1680.1660.205RANDOM17.224
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]
0.460.230.46-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.868
r_dihedral_angle_3_deg11.59
r_dihedral_angle_4_deg10.886
r_scangle_it7.008
r_dihedral_angle_1_deg5.515
r_scbond_it4.969
r_mcangle_it3.288
r_mcbond_it2.032
r_angle_refined_deg1.611
r_angle_other_deg1.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.868
r_dihedral_angle_3_deg11.59
r_dihedral_angle_4_deg10.886
r_scangle_it7.008
r_dihedral_angle_1_deg5.515
r_scbond_it4.969
r_mcangle_it3.288
r_mcbond_it2.032
r_angle_refined_deg1.611
r_angle_other_deg1.101
r_mcbond_other0.583
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3693
Nucleic Acid Atoms
Solvent Atoms425
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing