1VLJ

Crystal structure of NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O2DTM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP5.72930.2M NaCl, 0.2% PEG-1000, 0.1M Na,K-Phosphate pH 5.7 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.691α = 90
b = 129.699β = 103.61
c = 55.234γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2003-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.785093.950.04121.672.856578536.93
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8468.720.3381.941.874773

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 REPLACEMENTTHROUGHOUTTM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920)1.7849.662407334393.860.144750.142240.19265RANDOM35.944
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]
-0.381.73-0.471.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.7
r_dihedral_angle_4_deg15.307
r_dihedral_angle_3_deg13.591
r_scangle_it7.306
r_dihedral_angle_1_deg5.671
r_scbond_it5.538
r_mcangle_it2.962
r_mcbond_it2.249
r_angle_refined_deg1.562
r_angle_other_deg1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.7
r_dihedral_angle_4_deg15.307
r_dihedral_angle_3_deg13.591
r_scangle_it7.306
r_dihedral_angle_1_deg5.671
r_scbond_it5.538
r_mcangle_it2.962
r_mcbond_it2.249
r_angle_refined_deg1.562
r_angle_other_deg1
r_mcbond_other0.617
r_symmetry_vdw_other0.265
r_nbd_refined0.234
r_symmetry_vdw_refined0.211
r_nbd_other0.18
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.15
r_chiral_restr0.099
r_nbtor_other0.087
r_xyhbond_nbd_other0.061
r_bond_refined_d0.017
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 Atoms6078
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms98

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement