6PEI

Structure of sorbitol dehydrogenase from Sinorhizobium meliloti 1021


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E6P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429350 mM sodium acetate, 100 mM HEPES pH 7.4, 18% PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.969α = 90
b = 89.391β = 118.12
c = 87.14γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++2016-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5419

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
12.143.799.80.1178.73.465492
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)
12.19.620.586

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 REPLACEMENTTHROUGHOUT4E6P2.139.2962151331499.720.19550.19240.2517RANDOM23.422
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]
0.46-0.89-0.440.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.772
r_dihedral_angle_4_deg16.804
r_dihedral_angle_3_deg15.691
r_dihedral_angle_1_deg6.936
r_angle_other_deg2.389
r_mcangle_it2.265
r_mcbond_it1.506
r_mcbond_other1.506
r_angle_refined_deg1.464
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.772
r_dihedral_angle_4_deg16.804
r_dihedral_angle_3_deg15.691
r_dihedral_angle_1_deg6.936
r_angle_other_deg2.389
r_mcangle_it2.265
r_mcbond_it1.506
r_mcbond_other1.506
r_angle_refined_deg1.464
r_chiral_restr0.065
r_bond_other_d0.037
r_gen_planes_other0.009
r_bond_refined_d0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7608
Nucleic Acid Atoms
Solvent Atoms737
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing