4DY6

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 2'-phosphate bis(adenosine)-5'-diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I2CPDB ENTRY 2I2C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42910.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v PEG400, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2946.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.1α = 90
b = 75.73β = 90
c = 118.85γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.933ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.263.88899.10.0480.04818.63.214651
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3294.50.460.461.62.11976

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 2I2C2.233.55148231465173798.840.20850.20630.2504RANDOM48.0938
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]
-0.320.89-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.992
r_dihedral_angle_4_deg20.062
r_dihedral_angle_3_deg15.595
r_dihedral_angle_1_deg6.301
r_scangle_it1.955
r_mcangle_it1.594
r_angle_other_deg1.378
r_angle_refined_deg1.293
r_scbond_it1.252
r_mcbond_it0.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.992
r_dihedral_angle_4_deg20.062
r_dihedral_angle_3_deg15.595
r_dihedral_angle_1_deg6.301
r_scangle_it1.955
r_mcangle_it1.594
r_angle_other_deg1.378
r_angle_refined_deg1.293
r_scbond_it1.252
r_mcbond_it0.878
r_mcbond_other0.108
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2058
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms62

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
AMoREphasing