3NTD

Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase C531S Mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.729850 mM Na acetate, 200 mM ammonium acetate, 5% PEG 8K, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3663.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.737α = 90
b = 133.737β = 90
c = 79.713γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.979SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9911699.30.09215.84.510326810326822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.0799.70.416.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3ICR1.99115.85108806103268553899.320.159580.158240.18465RANDOM33.884
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]
-22.26-22.2644.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.331
r_dihedral_angle_4_deg20.574
r_dihedral_angle_3_deg17.636
r_dihedral_angle_1_deg7.486
r_scangle_it5.531
r_scbond_it3.909
r_angle_refined_deg2.353
r_mcangle_it2.202
r_mcbond_it1.434
r_chiral_restr0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.331
r_dihedral_angle_4_deg20.574
r_dihedral_angle_3_deg17.636
r_dihedral_angle_1_deg7.486
r_scangle_it5.531
r_scbond_it3.909
r_angle_refined_deg2.353
r_mcangle_it2.202
r_mcbond_it1.434
r_chiral_restr0.186
r_bond_refined_d0.029
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8589
Nucleic Acid Atoms
Solvent Atoms607
Heterogen Atoms204

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing