3AAR

Crystal structure of Lp1NTPDase from Legionella pneumophila in complex with AMPPNP


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
2.9858.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.701α = 90
b = 104.701β = 90
c = 75.415γ = 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
11.653597.60.11914.37.555849
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)
1.651.7498.80.4523.57.3

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 3AAP1.652052982283896.920.177530.176450.19717RANDOM17.487
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]
0.480.240.48-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.835
r_dihedral_angle_4_deg20.056
r_dihedral_angle_3_deg12.365
r_dihedral_angle_1_deg5.097
r_scangle_it3.865
r_scbond_it2.886
r_mcangle_it1.758
r_mcbond_it1.445
r_angle_refined_deg1.26
r_chiral_restr0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.835
r_dihedral_angle_4_deg20.056
r_dihedral_angle_3_deg12.365
r_dihedral_angle_1_deg5.097
r_scangle_it3.865
r_scbond_it2.886
r_mcangle_it1.758
r_mcbond_it1.445
r_angle_refined_deg1.26
r_chiral_restr0.34
r_nbtor_refined0.31
r_symmetry_vdw_refined0.215
r_nbd_refined0.211
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.136
r_metal_ion_refined0.099
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2947
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms31

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling