3MOG

Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Escherichia coli K12 substr. MG1655


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5100MM TRIS-HCL, PH 8.5, 30% PEG 4K, 200MM SODIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.4549.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.302α = 90
b = 145.753β = 90
c = 148.783γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 315MIRRORS2009-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.24099.80.0697.85.180082-552.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.2499.90.85

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.22076421236799.320.217440.215930.2659RANDOM69.021
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]
-1.072.02-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.161
r_dihedral_angle_3_deg16.956
r_dihedral_angle_4_deg16.774
r_scangle_it7.827
r_scbond_it5.728
r_dihedral_angle_1_deg5.645
r_mcangle_it4.711
r_mcbond_it3.142
r_angle_refined_deg1.223
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.161
r_dihedral_angle_3_deg16.956
r_dihedral_angle_4_deg16.774
r_scangle_it7.827
r_scbond_it5.728
r_dihedral_angle_1_deg5.645
r_mcangle_it4.711
r_mcbond_it3.142
r_angle_refined_deg1.223
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10808
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms15

Software

Software
Software NamePurpose
SHELXmodel building
RESOLVEmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing