6FPW

Structure of fully reduced Hydrogenase (Hyd-1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LMM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.7296100 mM bis-tris pH 5.7 200 mM LiSO4 150 mM NaCl 19-22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.146.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.835α = 90
b = 97.729β = 90
c = 182.911γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.3597.71000.1137.87366570
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)
11.351.371001.161.36.9

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 REPLACEMENTTHROUGHOUT5LMM1.3591.463482471809099.90.1160.1140.144RANDOM16.78
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]
0.41-0.11-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_sphericity_free21.801
r_dihedral_angle_4_deg16.168
r_dihedral_angle_3_deg12.083
r_sphericity_bonded6.867
r_dihedral_angle_1_deg5.956
r_rigid_bond_restr2.806
r_long_range_B_refined2.789
r_scangle_other2.63
r_long_range_B_other2.548
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_sphericity_free21.801
r_dihedral_angle_4_deg16.168
r_dihedral_angle_3_deg12.083
r_sphericity_bonded6.867
r_dihedral_angle_1_deg5.956
r_rigid_bond_restr2.806
r_long_range_B_refined2.789
r_scangle_other2.63
r_long_range_B_other2.548
r_scbond_it2.356
r_scbond_other2.356
r_angle_refined_deg1.661
r_mcangle_it1.58
r_mcangle_other1.58
r_mcbond_it1.342
r_mcbond_other1.342
r_angle_other_deg1.057
r_chiral_restr0.116
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
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 Atoms13165
Nucleic Acid Atoms
Solvent Atoms1272
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing