6K37

Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29328% PEG 3350, 0.2M Ammonium formate, 0.1M HEPES-NaOH (pH7.0), 5mM 3-(1-aminoethyl)-nonanedioic acid, 5mM NAD+
Crystal Properties
Matthews coefficientSolvent content
1.8734.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.414α = 90
b = 70.414β = 90
c = 98.778γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702018-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
12.5501000.10.0340.99328.59.610264
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)
12.52.540.6460.2120.901

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 REPLACEMENTTHROUGHOUT6ITD2.538.41975448699.940.177970.173680.26874RANDOM54.314
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]
1.040.521.04-3.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.496
r_dihedral_angle_3_deg19.746
r_dihedral_angle_4_deg11.755
r_long_range_B_other8.378
r_long_range_B_refined8.377
r_dihedral_angle_1_deg7.397
r_scangle_other6.383
r_mcangle_it5.296
r_mcangle_other5.294
r_scbond_other4.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.496
r_dihedral_angle_3_deg19.746
r_dihedral_angle_4_deg11.755
r_long_range_B_other8.378
r_long_range_B_refined8.377
r_dihedral_angle_1_deg7.397
r_scangle_other6.383
r_mcangle_it5.296
r_mcangle_other5.294
r_scbond_other4.183
r_scbond_it4.181
r_mcbond_it3.708
r_mcbond_other3.699
r_angle_refined_deg1.473
r_angle_other_deg1.311
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.003
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 Atoms2447
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing