4BRF

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with a distorted orthomolybdate ion and AMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.4100MM NA+ MES PH 5.4, 100MM NACL, 14% PEG3350, 20MM MGCL2, 50MM MGSO4
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.144α = 90
b = 85.97β = 106.14
c = 71.888γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.630980.0713.45.193825-318.4

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.629.8792408138797.90.126310.125460.1843RANDOM23.786
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]
-0.09-0.22-0.940.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.388
r_sphericity_free33.308
r_dihedral_angle_4_deg22.034
r_sphericity_bonded21.481
r_dihedral_angle_3_deg13.965
r_dihedral_angle_1_deg6.037
r_rigid_bond_restr5.674
r_angle_refined_deg1.839
r_chiral_restr0.124
r_bond_refined_d0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.388
r_sphericity_free33.308
r_dihedral_angle_4_deg22.034
r_sphericity_bonded21.481
r_dihedral_angle_3_deg13.965
r_dihedral_angle_1_deg6.037
r_rigid_bond_restr5.674
r_angle_refined_deg1.839
r_chiral_restr0.124
r_bond_refined_d0.02
r_gen_planes_refined0.01
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5716
Nucleic Acid Atoms
Solvent Atoms547
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement