6FPO

High resolution structure of native Hydrogenase (Hyd-1)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.1293100 mM tris pH 8.1 200 mM LiSO4 150 mM NaCl 20-22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.146.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.786α = 90
b = 97.733β = 90
c = 183.102γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.7749DiamondI02

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
11.0599.5599.80.11711.313.1773665
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)
11.051.0799.22.211.411.3

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 REPLACEMENTTHROUGHOUT4USC1.0591.557336413860799.70.1160.1150.134RANDOM12.24
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]
0.140.01-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.378
r_sphericity_free20.682
r_dihedral_angle_4_deg18.056
r_dihedral_angle_3_deg11.747
r_sphericity_bonded7.343
r_dihedral_angle_1_deg6.195
r_rigid_bond_restr3.428
r_long_range_B_refined2.732
r_scangle_other2.449
r_long_range_B_other2.409
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.378
r_sphericity_free20.682
r_dihedral_angle_4_deg18.056
r_dihedral_angle_3_deg11.747
r_sphericity_bonded7.343
r_dihedral_angle_1_deg6.195
r_rigid_bond_restr3.428
r_long_range_B_refined2.732
r_scangle_other2.449
r_long_range_B_other2.409
r_scbond_it2.2
r_scbond_other2.2
r_angle_refined_deg1.844
r_mcangle_it1.193
r_mcangle_other1.193
r_angle_other_deg1.135
r_mcbond_it0.98
r_mcbond_other0.98
r_chiral_restr0.134
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13162
Nucleic Acid Atoms
Solvent Atoms1748
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing