1Y60

Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1 with bound 5,10-methylene tetrahydromethanopterin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y5YFormaldehyde-activating enzyme from Methylobacterium extorquens AM1 PDB ID 1Y5Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52810.1 M HEPES/NaOH pH 7.5, 20% (w/v) polyethyleneglycol 10,000, 5 mM tetrahydromethanopterin (H4MPT), VAPOR DIFFUSION, HANGING DROP, temperature 281.0K
Crystal Properties
Matthews coefficientSolvent content
238

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.86α = 90
b = 112.59β = 91
c = 72.01γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 4r2003-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.939270ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.944.8293.50.1440.08212.153.75951657191-320.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.92.0176.10.50.43.033.28288

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 REPLACEMENTTHROUGHOUTFormaldehyde-activating enzyme from Methylobacterium extorquens AM1 PDB ID 1Y5Y1.944.825719157191296796.90.2250.2250.2090.241RANDOM29
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]
18.766.46-9.77-8.99
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_scangle_it4.66
c_scbond_it3.53
c_mcangle_it2.97
c_mcbond_it2.32
c_angle_deg1.6
c_improper_angle_d1.07
c_bond_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6293
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms225

Software

Software
Software NamePurpose
DENZOdata reduction
XDSdata reduction
EPMRphasing
CNSrefinement
XDSdata scaling