3GDL

Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GDKPDB entry 3GDK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629330% PEG 2000, 0.1M Sodium acetate, 0.2M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.6353.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.73α = 90
b = 80.356β = 125.12
c = 77.566γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97915NSLSX4A

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
11.652595.50.067695986959815.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3GDK1.6524.96959869598350095.50.2010.2010.20.227RANDOM17.5
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]
74.36-6.79-0.21
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.4
c_scangle_it2.66
c_scbond_it1.9
c_mcangle_it1.38
c_angle_deg1.3
c_mcbond_it0.97
c_improper_angle_d0.77
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3956
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms42

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling