4BVP

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with heptamolybdate and octamolybdate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1100MM NAMES PH 5.2, 11% PEG3350, 20MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.564α = 90
b = 85.436β = 103.94
c = 71.779γ = 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
11.4945.396.50.0618.46.1119751-312.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT1.4945.34118516120796.330.126520.126080.16858RANDOM17.175
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]
0.1-0.590.96-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.904
r_sphericity_free27.655
r_dihedral_angle_4_deg19.176
r_sphericity_bonded16.816
r_dihedral_angle_3_deg12.132
r_dihedral_angle_1_deg5.954
r_rigid_bond_restr4.682
r_angle_refined_deg2.577
r_chiral_restr0.12
r_bond_refined_d0.021
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.904
r_sphericity_free27.655
r_dihedral_angle_4_deg19.176
r_sphericity_bonded16.816
r_dihedral_angle_3_deg12.132
r_dihedral_angle_1_deg5.954
r_rigid_bond_restr4.682
r_angle_refined_deg2.577
r_chiral_restr0.12
r_bond_refined_d0.021
r_gen_planes_refined0.011
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 Atoms5856
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms282

Software

Software
Software NamePurpose
REFMACrefinement