3LLD

Crystal structure of the mutant S127G 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 3G18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729320% PEG 3350, 0.15M malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.1241.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.779α = 90
b = 63.638β = 115.19
c = 61.119γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-04-17MSINGLE 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
11.452593.40.064687026870214.3

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 REPLACEMENTTHROUGHOUT3G181.4522.76870268702344493.40.1860.1840.1840.216RANDOM15.4
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]
-2.34-0.642.090.24
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it2.76
c_scbond_it1.9
c_mcangle_it1.43
c_angle_deg1.2
c_mcbond_it0.96
c_improper_angle_d0.87
c_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3295
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms42

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling