2Q5F

Crystal structure of LMNADK1 from Listeria monocytogenes


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291PEG400 15-20% w/v, KCitrate 50 mM, KCl 300 mM, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2645.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.959α = 90
b = 75.088β = 90
c = 118.49γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.928.287.50.060.06320.25.9220001966329.25
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)
11.91.9951.60.4892.53.91644

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB2I2C1.928.2225281906658987.220.189140.189140.188150.22181RANDOM27.827
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]
-0.52.42-1.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.533
r_dihedral_angle_4_deg25.401
r_dihedral_angle_1_deg21.375
r_dihedral_angle_3_deg17.385
r_angle_other_deg1.615
r_scangle_it1.6
r_scbond_it1.431
r_angle_refined_deg1.43
r_mcangle_it0.847
r_mcbond_it0.692
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.533
r_dihedral_angle_4_deg25.401
r_dihedral_angle_1_deg21.375
r_dihedral_angle_3_deg17.385
r_angle_other_deg1.615
r_scangle_it1.6
r_scbond_it1.431
r_angle_refined_deg1.43
r_mcangle_it0.847
r_mcbond_it0.692
r_symmetry_vdw_other0.292
r_nbd_refined0.217
r_nbd_other0.212
r_symmetry_hbond_refined0.185
r_nbtor_refined0.178
r_symmetry_vdw_refined0.16
r_xyhbond_nbd_refined0.118
r_nbtor_other0.098
r_mcbond_other0.091
r_chiral_restr0.089
r_bond_refined_d0.01
r_bond_other_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2056
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing