2P5Y

Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P5UPDB entry 2P5U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.71 mg/ml) AND RESERVOIR SOLUTION CONTAINING 1.0M Magnesium sulfate, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0760

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.667α = 90
b = 135.667β = 90
c = 135.667γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2007-03-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.97928APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.92501000.06815.242.43316433164
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)
1.921.991000.31241.43230

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2P5U1.92303306433064167399.950.1920.1910.207RANDOM25.125
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.207
r_dihedral_angle_4_deg15.544
r_dihedral_angle_3_deg13.564
r_dihedral_angle_1_deg5.335
r_scangle_it3.557
r_scbond_it2.193
r_mcangle_it1.343
r_angle_refined_deg1.282
r_mcbond_it0.89
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.207
r_dihedral_angle_4_deg15.544
r_dihedral_angle_3_deg13.564
r_dihedral_angle_1_deg5.335
r_scangle_it3.557
r_scbond_it2.193
r_mcangle_it1.343
r_angle_refined_deg1.282
r_mcbond_it0.89
r_nbtor_refined0.306
r_nbd_refined0.188
r_symmetry_vdw_refined0.168
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.112
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2387
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms44

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
EPMRphasing