5A4M

Mechanism of Hydrogen activation by NiFe-hydrogenases


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.20.2 M NA/K TARTRATE, 20% (W/V) PEG 3350, pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.3146.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.671α = 90
b = 97.162β = 90
c = 182.911γ = 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 I04DiamondI04

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
11.746.999.10.19.85.6181455-3
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)
11.71.7398.21.041.65.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3USC1.791.62172419897998.940.135640.134250.16235RANDOM21
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]
-0.011.32-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.904
r_dihedral_angle_4_deg17.443
r_dihedral_angle_3_deg12.526
r_dihedral_angle_1_deg6.105
r_scangle_it4.135
r_angle_refined_deg2.256
r_scbond_it2.094
r_angle_other_deg1.585
r_mcangle_it1.547
r_mcbond_it1.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.904
r_dihedral_angle_4_deg17.443
r_dihedral_angle_3_deg12.526
r_dihedral_angle_1_deg6.105
r_scangle_it4.135
r_angle_refined_deg2.256
r_scbond_it2.094
r_angle_other_deg1.585
r_mcangle_it1.547
r_mcbond_it1.058
r_mcbond_other1.058
r_symmetry_vdw_refined0.31
r_nbd_refined0.278
r_xyhbond_nbd_other0.262
r_nbd_other0.232
r_nbtor_refined0.186
r_chiral_restr0.175
r_symmetry_vdw_other0.175
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.143
r_metal_ion_refined0.112
r_nbtor_other0.099
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.008
r_gen_planes_other0.005
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13133
Nucleic Acid Atoms
Solvent Atoms1492
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing