5ADU

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 6.0, 21 % PEG 3350, 200 MM LISO4, 150 MM NACL
Crystal Properties
Matthews coefficientSolvent content
2.1442.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.855α = 90
b = 98.979β = 90
c = 185.207γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMIRRORS2015-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.149.595.50.1610.512.8665775-3
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)
11.11.1292.11.51.712.3

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 3USC1.192.786323873329895.270.126930.126120.14238RANDOM10.686
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]
0.2-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.317
r_sphericity_free18.264
r_dihedral_angle_4_deg16.302
r_dihedral_angle_3_deg11.911
r_dihedral_angle_1_deg6.112
r_sphericity_bonded5.275
r_rigid_bond_restr3.035
r_angle_refined_deg1.866
r_scangle_it1.662
r_scbond_it1.403
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.317
r_sphericity_free18.264
r_dihedral_angle_4_deg16.302
r_dihedral_angle_3_deg11.911
r_dihedral_angle_1_deg6.112
r_sphericity_bonded5.275
r_rigid_bond_restr3.035
r_angle_refined_deg1.866
r_scangle_it1.662
r_scbond_it1.403
r_angle_other_deg1.073
r_mcangle_it1.054
r_mcbond_it0.829
r_mcbond_other0.829
r_symmetry_vdw_refined0.244
r_xyhbond_nbd_other0.243
r_metal_ion_refined0.238
r_nbd_refined0.229
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.161
r_nbd_other0.152
r_symmetry_vdw_other0.139
r_chiral_restr0.107
r_symmetry_hbond_refined0.087
r_nbtor_other0.07
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms13163
Nucleic Acid Atoms
Solvent Atoms1093
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing