3KB6

Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DLDPDB ENTRY 2DLD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629825% PEG 200, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.938α = 90
b = 94.432β = 90
c = 188.849γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2007-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.10.98SRSPX10.1

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
12.123895.20.08812.288890224.4
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)
12.122.276.30.3065.36.17005

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2DLD2.123888512443995.310.1670.1640.212RANDOM29.453
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]
-1.453.13-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.69
r_dihedral_angle_4_deg15.89
r_dihedral_angle_3_deg13.287
r_dihedral_angle_1_deg5.963
r_scangle_it3.749
r_scbond_it2.347
r_angle_refined_deg1.494
r_mcangle_it1.429
r_angle_other_deg0.895
r_mcbond_it0.763
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.69
r_dihedral_angle_4_deg15.89
r_dihedral_angle_3_deg13.287
r_dihedral_angle_1_deg5.963
r_scangle_it3.749
r_scbond_it2.347
r_angle_refined_deg1.494
r_mcangle_it1.429
r_angle_other_deg0.895
r_mcbond_it0.763
r_mcbond_other0.198
r_chiral_restr0.087
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10697
Nucleic Acid Atoms
Solvent Atoms853
Heterogen Atoms452

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection