4BRQ

LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, IN COMPLEX WITH TWO PHOSPHATES BOUND TO ACTIVE SITE MG AND PRODUCT AMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15100MM NAMES PH 5.0, 13% PEG3350, 20MM MGCL2, 20MM ADP
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.737α = 90
b = 85.497β = 106.2
c = 70.336γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH RAYONIXMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.3BESSY14.3

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
11.452998.40.0813.16.6123883-313

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.4529.14122610123898.220.139230.138750.18711RANDOM17.607
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]
-0.470.58-0.820.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.738
r_sphericity_free31.62
r_sphericity_bonded17.65
r_dihedral_angle_4_deg15.511
r_dihedral_angle_3_deg12.517
r_dihedral_angle_1_deg5.82
r_rigid_bond_restr5.003
r_angle_refined_deg2.042
r_chiral_restr0.138
r_bond_refined_d0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.738
r_sphericity_free31.62
r_sphericity_bonded17.65
r_dihedral_angle_4_deg15.511
r_dihedral_angle_3_deg12.517
r_dihedral_angle_1_deg5.82
r_rigid_bond_restr5.003
r_angle_refined_deg2.042
r_chiral_restr0.138
r_bond_refined_d0.02
r_gen_planes_refined0.012
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 Atoms5734
Nucleic Acid Atoms
Solvent Atoms624
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement