4Z9R

Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YX6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.2 M potassium/sodium tartate, 0.1 M Bis tris propane at pH 8.5 and 20 % (w/v) polyethylene glycol.
Crystal Properties
Matthews coefficientSolvent content
2.5952.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.68α = 90
b = 106.68β = 90
c = 217.477γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M2013-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
12.848.4495.90.2789.64.7303579.6

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 REPLACEMENTTHROUGHOUT4YX62.848.4428792147795.330.214180.21220.2527RANDOM32.51
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]
1.261.26-2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.986
r_dihedral_angle_4_deg18.522
r_dihedral_angle_3_deg16.312
r_long_range_B_refined6.491
r_long_range_B_other6.491
r_scangle_other4.504
r_dihedral_angle_1_deg4.12
r_mcangle_other3.944
r_mcangle_it3.943
r_scbond_it2.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.986
r_dihedral_angle_4_deg18.522
r_dihedral_angle_3_deg16.312
r_long_range_B_refined6.491
r_long_range_B_other6.491
r_scangle_other4.504
r_dihedral_angle_1_deg4.12
r_mcangle_other3.944
r_mcangle_it3.943
r_scbond_it2.806
r_scbond_other2.806
r_mcbond_it2.439
r_mcbond_other2.437
r_angle_refined_deg0.805
r_angle_other_deg0.583
r_chiral_restr0.044
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7315
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling