3RLV

Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LTPPDB ENTRY 3LTP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529330% PEG400, 0.1 M HEPES, 0.2 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.141.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.625α = 90
b = 63.413β = 115.02
c = 61.038γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42011-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4ANSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.42141.12698.917677676776

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3LTP1.42141.1267677676776385698.910.17340.17230.1935RANDOM
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]
-3.3108-3.12733.5083-0.1975
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.789
f_angle_d1.069
f_chiral_restr0.073
f_plane_restr0.007
f_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3321
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms50

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling