5TJR

X-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas sp. AAC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZZ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.6281Protein at 5 mg/mL with added acetyl-CoA; crystal conditions were 100 mM bis-tris propane at pH 7.6, 24% PEG 3350, 210 mM trisodium citr ate in 150 plus 150 nL drops.
Crystal Properties
Matthews coefficientSolvent content
2.5451.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.891α = 90
b = 156.631β = 90
c = 192.246γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.9549.699.90.1780.99811.514.774332
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.011001.6070.818215

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 REPLACEMENTTHROUGHOUT4zz72.954970516371499.860.214170.212360.24862RANDOM72.029
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]
-4.137.93-3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.035
r_dihedral_angle_4_deg19.73
r_dihedral_angle_3_deg17.191
r_long_range_B_refined14.274
r_long_range_B_other14.274
r_scangle_other8.656
r_mcangle_other8.043
r_mcangle_it8.042
r_dihedral_angle_1_deg5.984
r_scbond_it5.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.035
r_dihedral_angle_4_deg19.73
r_dihedral_angle_3_deg17.191
r_long_range_B_refined14.274
r_long_range_B_other14.274
r_scangle_other8.656
r_mcangle_other8.043
r_mcangle_it8.042
r_dihedral_angle_1_deg5.984
r_scbond_it5.306
r_scbond_other5.306
r_mcbond_it5.171
r_mcbond_other5.166
r_angle_refined_deg1.686
r_angle_other_deg1.058
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms20813
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms135

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing