2J63

Crystal structure of AP endonuclease LMAP from Leishmania major


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP290HAMPTON SCREEN I CONDITION 42: 20% PEG 8000, 50MM POTASSIUM PHOSPHATE. HANGING DROPS AT 17C
Crystal Properties
Matthews coefficientSolvent content
1.9938.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.103α = 90
b = 45.009β = 116.79
c = 115.134γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2001-10-16MSINGLE 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
12.530.699.90.0517.530273053
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)
12.52.5499.80.242.637.3

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 1DE92.48105.4125926137899.20.2030.20.246RANDOM44.33
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]
-4.73-3.27-0.862.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_dihedral_angle_3_deg19.368
r_dihedral_angle_4_deg16.783
r_dihedral_angle_1_deg6.736
r_scangle_it2.193
r_angle_refined_deg1.409
r_scbond_it1.353
r_mcangle_it1.252
r_mcbond_it0.721
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_dihedral_angle_3_deg19.368
r_dihedral_angle_4_deg16.783
r_dihedral_angle_1_deg6.736
r_scangle_it2.193
r_angle_refined_deg1.409
r_scbond_it1.353
r_mcangle_it1.252
r_mcbond_it0.721
r_nbtor_refined0.312
r_xyhbond_nbd_refined0.247
r_nbd_refined0.226
r_symmetry_vdw_refined0.194
r_chiral_restr0.11
r_symmetry_hbond_refined0.102
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms5308
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing