3AAQ

Crystal structure of Lp1NTPDase from Legionella pneumophila in complex with the inhibitor ARL 67156


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AAPPDB ENTRY 3AAP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529420-24%(w/v) PEG 3350, 0.2M Na Formate, 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.7855.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.479α = 90
b = 101.479β = 90
c = 74.867γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.954Australian SynchrotronMX1

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
124099.90.08921.24.230076
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)
22.111000.3822.64.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3AAP234.4428211148697.520.186590.184630.2242RANDOM32.421
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]
0.090.050.09-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.81
r_dihedral_angle_3_deg15.638
r_dihedral_angle_4_deg10.635
r_dihedral_angle_1_deg5.677
r_scangle_it3.712
r_scbond_it2.376
r_mcangle_it1.655
r_angle_refined_deg1.479
r_mcbond_it0.98
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.81
r_dihedral_angle_3_deg15.638
r_dihedral_angle_4_deg10.635
r_dihedral_angle_1_deg5.677
r_scangle_it3.712
r_scbond_it2.376
r_mcangle_it1.655
r_angle_refined_deg1.479
r_mcbond_it0.98
r_nbtor_refined0.309
r_symmetry_hbond_refined0.243
r_symmetry_vdw_refined0.238
r_nbd_refined0.213
r_xyhbond_nbd_refined0.198
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2767
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms37

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling