4Q0S

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with ribitol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q0PPDB ENTRY 4Q0P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529310-16%(v/v) PEG400, 0.2M NaCl, 0.1M HEPES, 0.02M Hexaammine cobalt(III) chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.32α = 90
b = 106.36β = 90
c = 118.68γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VIIMirrors2012-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.9322.3199.80.05912.34.6229822298224.6
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)
11.9321000.3523.84.52277

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4Q0P1.9322.312298222982226899.70.2130.2110.2110.233RANDOM36.4
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]
1.86-4.772.92
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.9
c_scangle_it2.73
c_mcangle_it2.31
c_scbond_it1.94
c_mcbond_it1.41
c_angle_deg1.4
c_improper_angle_d0.87
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1930
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms28

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling