3DAF

The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BOJPDB ENTRY 2BOJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.528350% MPD, 0.1M TRIS/HCL, 20mM NH4H2PO4, cyanide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.6453.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.14α = 90
b = 97.14β = 90
c = 166.03γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2007-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99198SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.75300.9010.0650.06518.36.13672936729
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.873.10.490.5145.22389

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BOJ1.75103667336673194496.310.18830.18830.186530.22154RANDOM34.124
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]
0.20.2-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.785
r_dihedral_angle_4_deg19.369
r_dihedral_angle_3_deg14.394
r_dihedral_angle_1_deg5.372
r_scangle_it4.057
r_scbond_it2.613
r_angle_refined_deg1.722
r_mcangle_it1.541
r_mcbond_it1.064
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.785
r_dihedral_angle_4_deg19.369
r_dihedral_angle_3_deg14.394
r_dihedral_angle_1_deg5.372
r_scangle_it4.057
r_scbond_it2.613
r_angle_refined_deg1.722
r_mcangle_it1.541
r_mcbond_it1.064
r_nbtor_refined0.3
r_nbd_refined0.214
r_chiral_restr0.21
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.155
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2591
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
EPMRphasing