4BVO

Legionella pneumophila NTPDase1 crystal form VI (part-open) in complex with polytungstate POM-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1100MM TRIS PH 7.3, 200MM K NA TARTRATE, 18% PEG3350, 10MM POM1
Crystal Properties
Matthews coefficientSolvent content
2.670.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.692α = 90
b = 143.692β = 90
c = 75.166γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.729.499.30.118.114.550327-3

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.7124.4449027129398.740.150360.149070.19757RANDOM24.184
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]
0.460.230.46-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.156
r_sphericity_free28.903
r_sphericity_bonded18.479
r_dihedral_angle_4_deg17.207
r_dihedral_angle_3_deg12.4
r_dihedral_angle_1_deg5.376
r_long_range_B_refined5.293
r_scbond_it4.301
r_mcangle_it3.625
r_rigid_bond_restr2.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.156
r_sphericity_free28.903
r_sphericity_bonded18.479
r_dihedral_angle_4_deg17.207
r_dihedral_angle_3_deg12.4
r_dihedral_angle_1_deg5.376
r_long_range_B_refined5.293
r_scbond_it4.301
r_mcangle_it3.625
r_rigid_bond_restr2.911
r_mcbond_it2.831
r_angle_refined_deg1.42
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2840
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement