6V45

Crystal structure of a Probable carnitine operon oxidoreductase caia from Brucella melitensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E5LMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 3ZGPMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 4A1KMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 4QRBMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 1ZATMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 6NTWMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 4XVOMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 6D5AMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 4LZHMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental modelPDB 4Z7AMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290Optimization screen around condition Anatrace MCSG1_E6, well C4: 18.9% (w/V) PEG 3350, 200mM Potassium sulfate: BrmeA.18116.b.B2.PS01846 at 18.1mg/ml: tray 312854c4, cryo: 20% EG in 2 steps: puck xvm4-2.
Crystal Properties
Matthews coefficientSolvent content
3.1761.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.06α = 90
b = 96.06β = 90
c = 96.06γ = 90
Symmetry
Space GroupP 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002019-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.65099.90.0440.0470.99927.757.36935471.381
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.671000.6390.6870.86237.511

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEMR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A2.642.961.35935293499.960.20230.19860.2346088.67
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d27.0533
f_angle_d0.7077
f_chiral_restr0.0517
f_bond_d0.0048
f_plane_restr0.0043
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1251
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms10

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MR-Rosettaphasing