5OK4

Crystal structure of native [Fe]-hydrogenase Hmd from Methanothermobacter marburgensis inactivated by O2.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JJF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7281.151-ml mixture containing 120 mM potassium phosphate pH 6.0, 1 mM EDTA, 26 uM (1 mg/ml) [Fe]-hydrogenase and 26 uM methylene-H4MPT was incubated in 5-ml amber vials with rubber stoppers under a gas mixture of N2/O2/H2 (70%/20%/10%) at 40 degree Celsius for 1 h. The inactivated enzyme was concentrated to 25 mg/ml using a 30 kDa centrifugal filter (Millipore). 0.7-ul of 25 mg/ml O2-inactivated [Fe]-hydrogenase was mixed with 0.7 ul of reservoir solution of 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, and 200 mM LiSO4. The best diffracting crystal was obtained in one month. Prior to freezing the crystal was soaked for 3 seconds in 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, 200 mM LiSO4 and 30% glycerol v/v.
Crystal Properties
Matthews coefficientSolvent content
2.9358.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.418α = 90
b = 127.418β = 90
c = 141.211γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00005SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.2947.071000.0480.018119.68.2110077
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.291.361001.1280.4230.6381.98

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-VALUE2JJF1.2943.4741.34110053544899.950.1280.1270.147121
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_d24.265
f_angle_d1.194
f_chiral_restr0.086
f_bond_d0.01
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2639
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms46

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing