6RP2

Threonine to Cysteine (T225C) variant of E coli hydrogenase-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9295100 mM Bis-tris pH 5.9 200 mM LiSO4 150 mM NaCl 18-21% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2344.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.72α = 90
b = 97.52β = 90
c = 183.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.3586.299.60.1350.0370.99911.412.5363874
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.37961.540.550.40.97.2

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 REPLACEMENTTHROUGHOUT1.3586.073456621809799.530.141930.141020.15926RANDOM13.837
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]
0.140.15-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.857
r_dihedral_angle_4_deg18.223
r_dihedral_angle_3_deg11.864
r_dihedral_angle_1_deg6.524
r_long_range_B_refined4.123
r_long_range_B_other3.956
r_scangle_other3.016
r_scbond_other2.047
r_scbond_it2.046
r_angle_refined_deg1.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.857
r_dihedral_angle_4_deg18.223
r_dihedral_angle_3_deg11.864
r_dihedral_angle_1_deg6.524
r_long_range_B_refined4.123
r_long_range_B_other3.956
r_scangle_other3.016
r_scbond_other2.047
r_scbond_it2.046
r_angle_refined_deg1.885
r_angle_other_deg1.64
r_mcangle_it1.347
r_mcangle_other1.347
r_mcbond_it0.967
r_mcbond_other0.967
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13160
Nucleic Acid Atoms
Solvent Atoms1520
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing