6PEJ

Structure of sorbitol dehydrogenase from Sinorhizobium meliloti 1021 bound to sorbitol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6PEI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29350 mM sodium acetate, 100 mM HEPES pH 7.4, 18% PEG 3000, 20% sorbitol
Crystal Properties
Matthews coefficientSolvent content
2.3146.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.298α = 90
b = 88.298β = 117.39
c = 87.317γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++2017-04-19MSINGLE 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
1239.6980.1395.4374395
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)
12100.522

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 REPLACEMENTTHROUGHOUT6PEI239.0870800358197.920.19680.19410.2494RANDOM19.442
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]
0.99-1.58-0.010.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.743
r_dihedral_angle_4_deg19.488
r_dihedral_angle_3_deg16.796
r_dihedral_angle_1_deg7.256
r_mcangle_it2.581
r_angle_other_deg2.469
r_angle_refined_deg1.927
r_mcbond_it1.848
r_mcbond_other1.848
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.743
r_dihedral_angle_4_deg19.488
r_dihedral_angle_3_deg16.796
r_dihedral_angle_1_deg7.256
r_mcangle_it2.581
r_angle_other_deg2.469
r_angle_refined_deg1.927
r_mcbond_it1.848
r_mcbond_other1.848
r_chiral_restr0.1
r_bond_other_d0.037
r_bond_refined_d0.015
r_gen_planes_other0.015
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7588
Nucleic Acid Atoms
Solvent Atoms905
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing