3G24

Crystal structure of the mutant D70N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G1Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529325% PEG 3350, 0.1M tris, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.592α = 90
b = 63.782β = 115.03
c = 61.293γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-11-16MSINGLE 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
11.525910.083606956069516.9

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 REPLACEMENTTHROUGHOUT3G1Y1.524.8660695606953049910.1850.1830.1830.197RANDOM16.6
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]
-3.3-0.551.661.64
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it2.84
c_scbond_it1.94
c_mcangle_it1.48
c_angle_deg1.2
c_mcbond_it1
c_improper_angle_d0.88
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3299
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms42

Software

Software
Software NamePurpose
APEXdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling