2B0J

The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIn-house Se-MAD model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5283Hepes/NaOH, 2-propanol, PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.3747.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.47α = 90
b = 59.88β = 90
c = 68.49γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97858SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.754099.60.07514.13.83854138541
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.79599.80.642.542820

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTstructure of Hmd from Methanopyrus kandleri1.75403854136576193399.590.1930.191460.21679RANDOM32.395
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]
-1.20.091.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.716
r_dihedral_angle_4_deg23.446
r_dihedral_angle_3_deg17.206
r_dihedral_angle_1_deg5.059
r_scangle_it3.995
r_scbond_it2.558
r_angle_refined_deg1.54
r_mcangle_it1.411
r_mcbond_it0.959
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.716
r_dihedral_angle_4_deg23.446
r_dihedral_angle_3_deg17.206
r_dihedral_angle_1_deg5.059
r_scangle_it3.995
r_scbond_it2.558
r_angle_refined_deg1.54
r_mcangle_it1.411
r_mcbond_it0.959
r_nbtor_refined0.312
r_nbd_refined0.23
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.136
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2593
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
EPMRphasing