1KEP

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G1APDB 1G1A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.429335% PEG 4000, 0.1M Citric acid pH 5.4, 0.3M ammonium sulphate and 3% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal Properties
Matthews coefficientSolvent content
3.6165.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.449α = 90
b = 97.182β = 90
c = 185.471γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4morrors2001-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.870SRSPX9.6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.891.3970.0940.0796.93.31020809182615.82
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.985.10.3640.2912.52.312822

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 1G1A1.891.29102080918261015196.830.147950.145250.17238RANDOM6.427
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]
0.030.32-0.35
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it4.132
p_scbond_it2.565
p_angle_d1.771
p_angle_deg1.771
p_mcangle_it1.472
p_mcbond_it0.802
p_bond_d0.019
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5478
Nucleic Acid Atoms
Solvent Atoms804
Heterogen Atoms149

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling