6YKA

Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5283.15[Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml reconstituted holoenzyme was mixed with 0.7-ul reservoir solution under yellow light and incubated under dark conditions. The crystals grew within two weeks in 30% w/v polyethylene glycol 4000, 200-mM lithium sulfate and 100-mM Tris pH 8.5 (JBScreen Wizard 3&4 HTS, Jena Bioscience).
Crystal Properties
Matthews coefficientSolvent content
2.141.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.481α = 90
b = 79.481β = 90
c = 179.337γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97980ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.168.8331000.0590.0620.019128.810.83918141.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.211000.7110.7110.7460.2220.7551.111.1

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 REPLACEMENTTHROUGHOUT4JJF2.139.7439126187699.90.1970.1950.235RANDOM61.86
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]
-0.4312-0.43120.8623
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.57
t_omega_torsion1.66
t_angle_deg1.01
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.57
t_omega_torsion1.66
t_angle_deg1.01
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
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 Atoms5196
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms103

Software

Software
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing