7BC1

Crystal structure of aldo-keto reductase from Agrobacterium tumefaciens in a ternary complex with NADPH and glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BBY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1 M SPG 25% PEG 1500 In-drop protein concentration of 13 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.232845844.947571

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.853α = 90
b = 82.853β = 90
c = 77.255γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.552.571000.0820.0860.0250.99914.711.948238
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.91.671.770.5820.7469

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 REPLACEMENTTHROUGHOUT7BBY1.552.5145844236899.960.16720.16580.1945RANDOM21.006
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]
-1.19-0.59-1.193.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.731
r_dihedral_angle_4_deg17.249
r_dihedral_angle_3_deg11.707
r_dihedral_angle_1_deg6.082
r_angle_refined_deg1.725
r_angle_other_deg1.532
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.731
r_dihedral_angle_4_deg17.249
r_dihedral_angle_3_deg11.707
r_dihedral_angle_1_deg6.082
r_angle_refined_deg1.725
r_angle_other_deg1.532
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2178
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing