1WLT

Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue from Sulfolobus tokodaii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DZRPDB ENTRY 1DZR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529315% PEG 3350, 0.1M Sodium cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.549.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.147α = 90
b = 73.145β = 90
c = 126.242γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 4MONOCHROMETER2004-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0000Photon FactoryBL-6A

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
11.895099.90.0615.56.63581135811-324.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.891.9699.70.3796.436.33486

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 1DZR1.92033411175999.980.199570.197050.2463RANDOM26.019
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]
0.87-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.914
r_scangle_it5.327
r_scbond_it3.488
r_mcangle_it2.312
r_angle_refined_deg2.137
r_mcbond_it1.392
r_angle_other_deg1.011
r_symmetry_hbond_refined0.31
r_symmetry_vdw_other0.297
r_nbd_other0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.914
r_scangle_it5.327
r_scbond_it3.488
r_mcangle_it2.312
r_angle_refined_deg2.137
r_mcbond_it1.392
r_angle_other_deg1.011
r_symmetry_hbond_refined0.31
r_symmetry_vdw_other0.297
r_nbd_other0.26
r_nbd_refined0.194
r_symmetry_vdw_refined0.164
r_xyhbond_nbd_refined0.163
r_chiral_restr0.147
r_nbtor_other0.094
r_bond_refined_d0.03
r_gen_planes_other0.015
r_gen_planes_refined0.014
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2915
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling
MOLREPphasing