6GGU

Crystal structure of native FE-hydrogenase from Methanothermobacter marburgensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JJF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293[Fe]-hydrogenase was crystallized under red light condition, in an anaerobic tent containing a gas phase of 100% N2 by the sitting drop vapuor diffusion method. The crystallization drops contained 0.7 ul of 30 mg.ml-1 protein and 2 mM methenyl-H4MPT+ mixed with 0.7 ul of 0.1 M MES pH 6.0 and 0.8 M ammonium sulfate and spotted on 96-well 2-drop MRC crystallization plates in polystyrene (Molecular Dimensions, Suffolk, UK). The best crystal appeared within 2.5 months.
Crystal Properties
Matthews coefficientSolvent content
3.7867.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.06α = 90
b = 144.06β = 90
c = 95.06γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97980ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.647.5399.90.3110.3230.0850.9899.214.61837338.86
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)
12.62.7499.70.9140.2440.4413.415

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4JJF2.625.841832896099.90.1910.1880.235RANDOM37.32
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]
-5.9975-5.997511.995
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion16.55
t_omega_torsion1.45
t_angle_deg1.03
t_bond_d0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion16.55
t_omega_torsion1.45
t_angle_deg1.03
t_bond_d0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2638
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms98

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing