9ER9 | pdb_00009er9

Hydrogenase-1 Ni-R state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UE3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8296100 mM tris pH8 200 mM LiSO4 150 mM NaCl 19-21% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.569α = 90
b = 97.065β = 90
c = 182.877γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.7749DiamondI03

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
11.493.571000.310.090.9966.513.6325817
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)
11.41.421003.921.10.4370.813.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.485.8843254641627699.9240.1650.16420.16720.17920.181613.212
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]
0.1651.28-1.445
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.627
r_dihedral_angle_3_deg14.138
r_dihedral_angle_2_deg7.64
r_dihedral_angle_1_deg6.495
r_lrange_it4.23
r_lrange_other4.094
r_scangle_it3.311
r_scangle_other3.31
r_scbond_it2.166
r_scbond_other2.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.627
r_dihedral_angle_3_deg14.138
r_dihedral_angle_2_deg7.64
r_dihedral_angle_1_deg6.495
r_lrange_it4.23
r_lrange_other4.094
r_scangle_it3.311
r_scangle_other3.31
r_scbond_it2.166
r_scbond_other2.166
r_angle_refined_deg1.61
r_mcangle_it1.539
r_mcangle_other1.539
r_angle_other_deg1.127
r_mcbond_it1.101
r_mcbond_other1.101
r_nbd_refined0.218
r_symmetry_nbd_other0.201
r_nbtor_refined0.179
r_nbd_other0.163
r_xyhbond_nbd_refined0.127
r_symmetry_xyhbond_nbd_other0.122
r_symmetry_xyhbond_nbd_refined0.107
r_metal_ion_refined0.098
r_chiral_restr0.086
r_symmetry_nbtor_other0.078
r_symmetry_nbd_refined0.049
r_gen_planes_other0.011
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13154
Nucleic Acid Atoms
Solvent Atoms1484
Heterogen Atoms165

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing