8BJ7

Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Hinact-like state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SG2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.6281.151 M Lithium chloride, 0.1 M Sodium acetate, 30 % Polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
1.831.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.328α = 90
b = 87.281β = 90
c = 88.977γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.8266PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.0444.52899.70.1190.99910.913183605
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.041.062.4470.4991.1

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6SG21.0444.528183502938199.6290.1580.15770.1671RANDOM11.42
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]
0.624-0.052-0.572
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.378
r_dihedral_angle_3_deg14.758
r_dihedral_angle_2_deg7.502
r_dihedral_angle_1_deg6.416
r_lrange_it3.745
r_lrange_other3.678
r_scangle_other2.916
r_scangle_it2.9
r_angle_refined_deg2.144
r_scbond_other2.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.378
r_dihedral_angle_3_deg14.758
r_dihedral_angle_2_deg7.502
r_dihedral_angle_1_deg6.416
r_lrange_it3.745
r_lrange_other3.678
r_scangle_other2.916
r_scangle_it2.9
r_angle_refined_deg2.144
r_scbond_other2.022
r_scbond_it2.007
r_mcangle_it1.625
r_mcangle_other1.625
r_mcbond_it1.14
r_mcbond_other1.137
r_angle_other_deg1.047
r_symmetry_nbd_refined0.278
r_nbd_refined0.262
r_symmetry_xyhbond_nbd_refined0.225
r_symmetry_nbd_other0.206
r_nbtor_refined0.188
r_nbd_other0.18
r_chiral_restr0.161
r_xyhbond_nbd_refined0.108
r_metal_ion_refined0.097
r_symmetry_nbtor_other0.084
r_bond_other_d0.044
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3721
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing