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3-methyladenine dna-glycosylase from Archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JHN PDB ENTRY 2JHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M BICINE, PH9.0 10% W/V PEG20000 2% V/V DIOXANE
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.89 α = 90 b = 48.85 β = 106.07 c = 104.46 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH 2006-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.9 50 99.9 0.07 11.4 2.9 53742 19.75
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 1.9 1.95 100 0.43 2.5 2.9
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 2JHN 1.9 12 50786 2711 99.8 0.184 0.181 0.1817 0.239 0.2369 RANDOM 20.57
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] -0.19 -0.19 0.18 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.745 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 14.673 r_dihedral_angle_1_deg 5.346 r_scangle_it 3.734 r_scbond_it 2.439 r_mcangle_it 1.533 r_angle_refined_deg 1.366 r_mcbond_it 1.055 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.745 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 14.673 r_dihedral_angle_1_deg 5.346 r_scangle_it 3.734 r_scbond_it 2.439 r_mcangle_it 1.533 r_angle_refined_deg 1.366 r_mcbond_it 1.055 r_nbtor_refined 0.303 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 4762 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing