Experiment: 3RF7

 3RF7

Crystal structure of an Iron-containing alcohol dehydrogenase (Sden_2133) from Shewanella denitrificans OS-217 at 2.12 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.92770.300M calcium chloride, 26.00% polyethylene glycol 400, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.074α = 90
b = 121.074β = 90
c = 275.666γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR2009-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
12.1229.9471000.1668.17.4583325833233.086
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)
12.122.181001.3881.3881.67.54226

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.1229.94758283295199.920.18260.18190.1968RANDOM38.9231
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]
1.281.28-2.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.185
r_dihedral_angle_4_deg23.458
r_dihedral_angle_3_deg13.581
r_dihedral_angle_1_deg5.623
r_scangle_it3.103
r_scbond_it2.091
r_angle_refined_deg1.411
r_mcangle_it1.332
r_angle_other_deg0.909
r_mcbond_it0.699
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2787
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms83

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
SHELXDphasing