3P52

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52954.25 M NaNitrate, 0.1 M Bis-Tris, 10 mM NAD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.4564.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.945α = 90
b = 120.945β = 90
c = 91.795γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRROR2010-07-31MMOLECULAR REPLACEMENT
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

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
12.74301000.07623.27.62069020690-374
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.742.81000.8822.37.71029

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 1XNH2.74301956319563105699.210.210840.209110.24451RANDOM72.083
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]
1.270.641.27-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.761
r_dihedral_angle_4_deg20.196
r_dihedral_angle_3_deg19.143
r_dihedral_angle_1_deg5.218
r_scangle_it4.636
r_scbond_it2.97
r_angle_refined_deg1.653
r_mcangle_it1.475
r_mcbond_it0.72
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.761
r_dihedral_angle_4_deg20.196
r_dihedral_angle_3_deg19.143
r_dihedral_angle_1_deg5.218
r_scangle_it4.636
r_scbond_it2.97
r_angle_refined_deg1.653
r_mcangle_it1.475
r_mcbond_it0.72
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.005
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 Atoms3577
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms16

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
CCP4model building
MrBUMPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CCP4phasing