6HAC

Crystal structure of [Fe]-hydrogenase (Hmd) holoenzyme from Methanococcus aeolicus (open form)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4281.15The reconstituted [Fe]-hydrogenase holoenzyme from M. aeolicus was crystallized in the anaerobic tent with gas phase 95%N2/5%H2 using 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK). For the initial screening, 0.7-ul of 24 mg/ml reconstituted [Fe]-hydrogenase was mixed with 0.7 ul of reservoir solution of crystallization kits under yellow light and incubated under the dark condition. The best diffracting crystal was obtained in one month in the crystallization reservoir solution containing 20% w/v polyethylene glycol 3350, 100-mM tri-sodium citrate pH 4.0 and 200-mM tri-sodium citrate.
Crystal Properties
Matthews coefficientSolvent content
3.7467.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.985α = 90
b = 136.985β = 90
c = 117.317γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-09-26MSINGLE 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
12.348.431000.1550.1610.0430.99917.913.72507839.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.421001.0231.0610.2810.6022.914

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 REPLACEMENTTHROUGHOUT4JJF2.326.622504312291000.1720.1710.192RANDOM43.63
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]
2.59332.5933-5.1866
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion13.75
t_omega_torsion2.27
t_angle_deg1.11
t_bond_d0.009
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_torsion13.75
t_omega_torsion2.27
t_angle_deg1.11
t_bond_d0.009
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 Atoms2567
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms66

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing