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Crystal structure of AP endonuclease LMAP from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DE9 PDB ENTRY 1DE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 HAMPTON SCREEN I CONDITION 42: 20% PEG 8000, 50MM POTASSIUM PHOSPHATE. HANGING DROPS AT 17C
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.103 α = 90 b = 45.009 β = 116.79 c = 115.134 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 MIRRORS 2001-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 30.6 99.9 0.05 17.5 30 27305 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.8 0.24 2.6 37.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DE9 2.48 105.41 25926 1378 99.2 0.203 0.2 0.2053 0.246 0.2525 RANDOM 44.33
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 -0.86 2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 19.368 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_1_deg 6.736 r_scangle_it 2.193 r_angle_refined_deg 1.409 r_scbond_it 1.353 r_mcangle_it 1.252 r_mcbond_it 0.721 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 19.368 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_1_deg 6.736 r_scangle_it 2.193 r_angle_refined_deg 1.409 r_scbond_it 1.353 r_mcangle_it 1.252 r_mcbond_it 0.721 r_nbtor_refined 0.312 r_xyhbond_nbd_refined 0.247 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.194 r_chiral_restr 0.11 r_symmetry_hbond_refined 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 5308 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing