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Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUI PDB entry 1EUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 1.3 M Potassium phosphate dibasic, 0.1 M Sodium acetate pH 4.5, 5 mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 56.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.32 α = 90 b = 75.32 β = 90 c = 105.703 γ = 120
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 MARMOSAIC 325 mm CCD Mirrors 2007-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91724 SSRL BL9-2
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 1.5 50 97.2 0.045 14.3 10.2 52821 21.8
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 1.5 1.55 79.9 0.62 1.5 5.3 4325
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 1EUI 1.5 37.66 52760 2693 97.21 0.139 0.138 0.1412 0.16 0.1597 RANDOM 15.353
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] 0.34 0.17 0.34 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.475 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 11.752 r_scangle_it 7.073 r_dihedral_angle_1_deg 5.926 r_scbond_it 4.406 r_mcangle_it 3.259 r_mcbond_it 2.033 r_angle_refined_deg 1.623 r_angle_other_deg 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.475 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 11.752 r_scangle_it 7.073 r_dihedral_angle_1_deg 5.926 r_scbond_it 4.406 r_mcangle_it 3.259 r_mcbond_it 2.033 r_angle_refined_deg 1.623 r_angle_other_deg 0.974 r_mcbond_other 0.682 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1933 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling