4BRL

Legionella pneumophila NTPDase1 crystal form III (closed) in complex with transition state mimic guanosine 5'-phosphovanadate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.4100MM NAMES PH 5.4, 100MM NACL, 12% PEG3350, 20MM MGCL2, 10MM GMP
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.994α = 90
b = 83.463β = 90
c = 109.289γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
11.62099.20.06145.797136-322

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.619.8895610143499.180.144990.144160.19773RANDOM26.001
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]
0.010.72-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.319
r_sphericity_free29.21
r_dihedral_angle_4_deg21.987
r_sphericity_bonded19.848
r_dihedral_angle_3_deg13.759
r_rigid_bond_restr6.249
r_dihedral_angle_1_deg5.895
r_angle_refined_deg1.847
r_chiral_restr0.135
r_bond_refined_d0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.319
r_sphericity_free29.21
r_dihedral_angle_4_deg21.987
r_sphericity_bonded19.848
r_dihedral_angle_3_deg13.759
r_rigid_bond_restr6.249
r_dihedral_angle_1_deg5.895
r_angle_refined_deg1.847
r_chiral_restr0.135
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 Atoms5723
Nucleic Acid Atoms
Solvent Atoms462
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement