3P4T

Crystal structure of a putative acyl-CoA dehydrogenase from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OIBPDB ENTRY 3OIB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290EBS PACT SCEEN F12: 0.2M Sodium malonate, 0.1M Bis Tris propane pH 6.5; MYSMA.00247.B.A1 PW28486 at 27mg/ml, ph 6.5, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3647.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.93α = 90
b = 64.75β = 112.04
c = 83.81γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.000ALS5.0.2

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
11.75096.40.04120.684.38866285434-326.81
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)
11.71.7493.90.2095.73.96578

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 3OIB1.719.8285373427196.50.1550.1530.185RANDOM16.71
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]
-0.8-0.160.510.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.682
r_dihedral_angle_4_deg18.496
r_dihedral_angle_3_deg11.821
r_dihedral_angle_1_deg5.354
r_scangle_it3.788
r_scbond_it2.35
r_angle_refined_deg1.563
r_mcangle_it1.446
r_angle_other_deg1.026
r_mcbond_it0.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.682
r_dihedral_angle_4_deg18.496
r_dihedral_angle_3_deg11.821
r_dihedral_angle_1_deg5.354
r_scangle_it3.788
r_scbond_it2.35
r_angle_refined_deg1.563
r_mcangle_it1.446
r_angle_other_deg1.026
r_mcbond_it0.814
r_mcbond_other0.25
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5704
Nucleic Acid Atoms
Solvent Atoms780
Heterogen Atoms114

Software

Software
Software NamePurpose
BOSdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling