6ABJ

The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J49 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298100 mM sodium acetate (pH 5.5), 8% PEG3350, and 50 mM magnesium chloride.
Crystal Properties
Matthews coefficientSolvent content
2.6854.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.1α = 90
b = 186.84β = 90
c = 90.34γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102013-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8652.2699.90.0970.040.99612.3768606
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.9699.20.8270.3490.7742.26.4

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 REPLACEMENTTHROUGHOUT1J491.8652.2665029346699.70.199850.19840.22691RANDOM37.809
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]
0.38-0.01-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.695
r_dihedral_angle_4_deg21.595
r_dihedral_angle_3_deg14.601
r_long_range_B_refined6.725
r_long_range_B_other6.724
r_dihedral_angle_1_deg5.914
r_scangle_other4.739
r_mcangle_it3.242
r_mcangle_other3.242
r_scbond_it3.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.695
r_dihedral_angle_4_deg21.595
r_dihedral_angle_3_deg14.601
r_long_range_B_refined6.725
r_long_range_B_other6.724
r_dihedral_angle_1_deg5.914
r_scangle_other4.739
r_mcangle_it3.242
r_mcangle_other3.242
r_scbond_it3.08
r_scbond_other3.079
r_mcbond_it2.358
r_mcbond_other2.342
r_angle_refined_deg1.72
r_angle_other_deg1.206
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5041
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALAdata scaling
ARP/wARPmodel building
iMOSFLMdata reduction
MOLREPphasing