2JC5

Apurinic Apyrimidinic (AP) endonuclease (NApe) from Neisseria Meningitidis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP924 WELL LINBRO PLATES USED FOR HANGING DROP EXPERIMENTS WITH 0.5 UL PROTEIN AND 0.5 UL WELL SOLUTION FOR THE DROPS. PROTEIN CONCENTRATION 20 MG/ML, IN 10 MM TRIS, PH 7.0 AND 100 MM NACL. THE WELL SOLUTION CONTAINED 20% PEG 20000, 0.1 M BICINE PH 9.0, 2% DIOXANE.
Crystal Properties
Matthews coefficientSolvent content
2.0138.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.156α = 90
b = 79.511β = 107.22
c = 41.045γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.53094.60.0618.33.535560-39.64
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5586.30.274.53.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BIX1.529.533541217741000.1230.120.159RANDOM8.98
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]
-0.3360.0220.654-0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.826
r_dihedral_angle_4_deg13.08
r_dihedral_angle_3_deg10.996
r_dihedral_angle_1_deg6.191
r_scangle_it2.868
r_mcangle_it2.506
r_scbond_it2.16
r_mcbond_it1.986
r_angle_refined_deg1.33
r_symmetry_vdw_refined0.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.826
r_dihedral_angle_4_deg13.08
r_dihedral_angle_3_deg10.996
r_dihedral_angle_1_deg6.191
r_scangle_it2.868
r_mcangle_it2.506
r_scbond_it2.16
r_mcbond_it1.986
r_angle_refined_deg1.33
r_symmetry_vdw_refined0.722
r_symmetry_hbond_refined0.479
r_nbd_refined0.263
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.161
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2073
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing