8HAP

Crystal structure of thermostable acetaldehyde dehydrogenase from hyperthermophilic archaeon Sulfolobus tokodaii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PQA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2293100 mM sodium phosphate dibasic/citric acid (pH 4.2), 200 mM sodium chloride, 10% (v/v) polyethylene glycol (PEG) 3000
Crystal Properties
Matthews coefficientSolvent content
2.5551.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.075α = 90
b = 75.356β = 124.64
c = 105.305γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU1.0000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.19786.635990.0870.1040.0569.93.45356353563
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3297.70.5880.5880.7040.3831.33.3

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 REPLACEMENTTHROUGHOUT3PQA2.246.650864269998.990.17020.1680.2136RANDOM36.577
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.738
r_dihedral_angle_4_deg20.502
r_dihedral_angle_3_deg16.709
r_dihedral_angle_1_deg7.086
r_angle_refined_deg1.56
r_angle_other_deg1.289
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.738
r_dihedral_angle_4_deg20.502
r_dihedral_angle_3_deg16.709
r_dihedral_angle_1_deg7.086
r_angle_refined_deg1.56
r_angle_other_deg1.289
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7176
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms72

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction