7SXM

Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M1V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931 uL of 24 mg/mL MCR was mixed with 1 uL of well solution (27% (w/v) PEG400, 0.18 M magnesium acetate, 0.25 M sodium chloride, and 0.10 M HEPES pH 7.5) to make a 2-uL sitting drop in a sealed well with 30 uL well solution. Yellowish green rod MCR crystals grew in two to four hrs. The entire crystallization plate was shipped to Advanced Light Source Beamline 8.2.2 for Xe- pressurization and data collection. The crystals used to determine Xe-derivatized structure were transferred from the sitting drop into 2-5 uL of paraffin oil briefly and then sealed in a steel chamber pressurized with xenon at 180 psi for 10 mins. The Xe-derivatized crystals were flash-cooled in liquid nitrogen for data collection immediately.
Crystal Properties
Matthews coefficientSolvent content
2.1542.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.956α = 90
b = 115.741β = 92.525
c = 123.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.5498ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.50369.63397.10.0869.8315162735.38
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5032.590.731

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3M1V2.50369.631.34151575757397.040.18030.17830.21839.81
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.6486
f_angle_d0.5307
f_chiral_restr0.0406
f_plane_restr0.0032
f_bond_d0.0022
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19038
Nucleic Acid Atoms
Solvent Atoms838
Heterogen Atoms207

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing