4Q0U

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribose


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
2.6854.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.73α = 90
b = 107.06β = 90
c = 118.89γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VIIMirrors2012-04-11MSINGLE 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
11.9861.599.10.05514.27.1214642146425.8
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)
11.982.051000.284.672164

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 4Q0P1.9861.452145821458213598.90.2220.2210.2210.237RANDOM33
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]
-0.91-2.853.75
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.4
c_scangle_it2.73
c_mcangle_it2.33
c_scbond_it1.92
c_mcbond_it1.44
c_angle_deg1.4
c_improper_angle_d0.84
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1930
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms58

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling