8QMN

[FeFe]-hydrogenase maturase HydE from T. maritima - dialysis experiment - empty structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 4000, Tris pH 8, LiSO4
Crystal Properties
Matthews coefficientSolvent content
2.2946.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.74α = 90
b = 83.63β = 90
c = 70.51γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2023-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM070.97951ESRFBM07

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.485498.50.99913.126.462674
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.520.257

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.4853.9159575313198.750.135280.133090.17695RANDOM21.466
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]
-1.832.26-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.72
r_dihedral_angle_1_deg5.961
r_dihedral_angle_2_deg5.886
r_long_range_B_refined4.676
r_long_range_B_other3.898
r_rigid_bond_restr3.299
r_scangle_other2.244
r_angle_refined_deg1.812
r_mcangle_it1.789
r_mcangle_other1.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.72
r_dihedral_angle_1_deg5.961
r_dihedral_angle_2_deg5.886
r_long_range_B_refined4.676
r_long_range_B_other3.898
r_rigid_bond_restr3.299
r_scangle_other2.244
r_angle_refined_deg1.812
r_mcangle_it1.789
r_mcangle_other1.789
r_scbond_it1.623
r_scbond_other1.619
r_mcbond_it1.316
r_mcbond_other1.315
r_angle_other_deg0.697
r_chiral_restr0.12
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2846
Nucleic Acid Atoms
Solvent Atoms482
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing