5A4I

The 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
16100 MM BIS TRIS PH 5.9, 22% (W/V) PEG 3350, 200 MM LISO4, 150 MM NACL, 1 MM TCEP, 0.02 % DDM
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.78α = 90
b = 97.58β = 90
c = 182.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2015-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.2332.5397.40.1215.213.4468877-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.2694.91.313.3

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 3USC1.2332.194451412365297.20.125070.12390.14689RANDOM14.032
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]
0.160.28-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.225
r_sphericity_free17.933
r_dihedral_angle_4_deg16.799
r_dihedral_angle_3_deg12.003
r_dihedral_angle_1_deg6.123
r_sphericity_bonded5.878
r_rigid_bond_restr2.641
r_angle_refined_deg1.895
r_scangle_it1.834
r_scbond_it1.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.225
r_sphericity_free17.933
r_dihedral_angle_4_deg16.799
r_dihedral_angle_3_deg12.003
r_dihedral_angle_1_deg6.123
r_sphericity_bonded5.878
r_rigid_bond_restr2.641
r_angle_refined_deg1.895
r_scangle_it1.834
r_scbond_it1.794
r_mcangle_it1.29
r_angle_other_deg1.098
r_mcbond_it1.086
r_mcbond_other1.086
r_symmetry_vdw_refined0.26
r_nbd_refined0.243
r_nbd_other0.225
r_symmetry_vdw_other0.219
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.126
r_chiral_restr0.115
r_symmetry_hbond_refined0.109
r_nbtor_other0.096
r_metal_ion_refined0.08
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13170
Nucleic Acid Atoms
Solvent Atoms935
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing