3TFX

Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29110% w/v 1,6-Hexanediol, 0.2M MgCl2 and 20% w/v Polyethylene glycol 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3647.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.396α = 90
b = 68.17β = 106.31
c = 63.93γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2010-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9795NSLSX29A

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
12.195099.50.10121.47.12742927429
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)
12.192.2798.90.1226.82716

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.19502600526005136098.430.207260.204870.20530.251860.2101RANDOM17.602
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]
-0.86-0.540.260.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.077
r_dihedral_angle_3_deg16.509
r_dihedral_angle_4_deg15.316
r_dihedral_angle_1_deg5.786
r_scangle_it3.47
r_scbond_it2.207
r_angle_refined_deg1.345
r_mcangle_it1.175
r_mcbond_it0.604
r_chiral_restr0.097
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3461
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms

Software

Software
Software NamePurpose
CBASSdata collection
SHELXmodel building
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
SHELXphasing