3AAP

Crystal Structure of Lp1NTPDase from Legionella pneumophila


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CJ1PDB ENTRY 3CJ1

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
2.9358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.779α = 90
b = 103.779β = 90
c = 75.419γ = 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
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.979APS23-ID-B

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
11.64099.90.08433.521.362027
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)
1.61.691000.4544.420.7

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 3CJ11.637.7258843314299.90.18930.188340.20668RANDOM21.226
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]
0.080.040.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.362
r_dihedral_angle_3_deg13.224
r_dihedral_angle_4_deg10.538
r_dihedral_angle_1_deg5.341
r_scangle_it4.274
r_scbond_it2.883
r_mcangle_it1.901
r_angle_refined_deg1.494
r_mcbond_it1.217
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.362
r_dihedral_angle_3_deg13.224
r_dihedral_angle_4_deg10.538
r_dihedral_angle_1_deg5.341
r_scangle_it4.274
r_scbond_it2.883
r_mcangle_it1.901
r_angle_refined_deg1.494
r_mcbond_it1.217
r_nbtor_refined0.315
r_nbd_refined0.223
r_symmetry_hbond_refined0.171
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.146
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2792
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling