3QIV

Crystal structure of a putative short-chain dehydrogenase or 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium paratuberculosis ATCC BAA-968 / K-10


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GVCPDB ENTRY 3GVC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.528916.94 mg/ml MypaA.00414.c.A1, 300 mM magnessium formate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.44α = 90
b = 90.07β = 90
c = 92.255γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
12.255099.10.055144.724019
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)
12.252.2999.70.3524.21183

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 3GVC2.2540.4723922122198.770.21730.21530.2564RANDOM36.868
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]
-0.030.06-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.972
r_dihedral_angle_4_deg18.058
r_dihedral_angle_3_deg13.605
r_dihedral_angle_1_deg5.129
r_scangle_it1.588
r_scbond_it0.941
r_angle_refined_deg0.877
r_angle_other_deg0.806
r_mcangle_it0.65
r_mcbond_it0.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.972
r_dihedral_angle_4_deg18.058
r_dihedral_angle_3_deg13.605
r_dihedral_angle_1_deg5.129
r_scangle_it1.588
r_scbond_it0.941
r_angle_refined_deg0.877
r_angle_other_deg0.806
r_mcangle_it0.65
r_mcbond_it0.342
r_chiral_restr0.05
r_mcbond_other0.05
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2826
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction