4UE3

The Mechanism of Hydrogen Activation by NiFe-hydrogenases and the Importance of the active site Arginine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3USC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293100 mM Bis tris pH 5.5-5.9, 150 mM NaCl 200 mM Li2SO4 19-21% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0640.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.521α = 90
b = 97.405β = 90
c = 183.229γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

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
11.448.75970.1313.113.1317004-3
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)
11.41.4275.31.351.710.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3usc1.448.753169241565896.8350.1410.13970.160212.322
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]
0.141-0.046-0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.294
r_dihedral_angle_4_deg16.799
r_dihedral_angle_3_deg12.032
r_dihedral_angle_1_deg6.558
r_lrange_it4.012
r_lrange_other3.918
r_scangle_it3.187
r_scangle_other3.187
r_scbond_other2.147
r_scbond_it2.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.294
r_dihedral_angle_4_deg16.799
r_dihedral_angle_3_deg12.032
r_dihedral_angle_1_deg6.558
r_lrange_it4.012
r_lrange_other3.918
r_scangle_it3.187
r_scangle_other3.187
r_scbond_other2.147
r_scbond_it2.146
r_angle_refined_deg2.091
r_angle_other_deg1.633
r_mcangle_it1.464
r_mcangle_other1.464
r_mcbond_other1.033
r_mcbond_it1.032
r_nbd_refined0.234
r_symmetry_nbd_refined0.234
r_symmetry_xyhbond_nbd_refined0.229
r_nbd_other0.214
r_symmetry_nbd_other0.185
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.157
r_metal_ion_refined0.112
r_chiral_restr0.103
r_symmetry_nbtor_other0.087
r_symmetry_xyhbond_nbd_other0.075
r_bond_refined_d0.014
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13166
Nucleic Acid Atoms
Solvent Atoms1340
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing