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Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 PEG 4000, HEPES-NaOH, NaCl, Dithio threitol., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.89 α = 90 b = 97.69 β = 90 c = 36.1 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH 2003-10-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.03 57.74 93.7 0.07 0.058 11.6 5 587271 116782 -3 13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.03 1.1 78.1 0.468 2.5 3.9 17208
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 1.03 40 110906 110906 5880 93.76 0.15889 0.15889 0.15762 0.2107 0.18275 0.2281 RANDOM 15.567
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] 0.09 -0.06 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.34 r_dihedral_angle_4_deg 15.511 r_dihedral_angle_3_deg 12.177 r_sphericity_free 7.537 r_dihedral_angle_1_deg 5.066 r_scangle_it 4.5 r_sphericity_bonded 3.732 r_scbond_it 3.657 r_mcangle_it 2.622 r_angle_other_deg 2.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.34 r_dihedral_angle_4_deg 15.511 r_dihedral_angle_3_deg 12.177 r_sphericity_free 7.537 r_dihedral_angle_1_deg 5.066 r_scangle_it 4.5 r_sphericity_bonded 3.732 r_scbond_it 3.657 r_mcangle_it 2.622 r_angle_other_deg 2.496 r_mcbond_it 2.297 r_rigid_bond_restr 1.726 r_angle_refined_deg 1.689 r_mcbond_other 1.034 r_symmetry_vdw_other 0.36 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.209 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.12 r_symmetry_hbond_refined 0.096 r_nbtor_other 0.095 r_bond_refined_d 0.015 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 2054 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling SHARP phasing