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Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XC8 PDB ENTRY 1XC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100 MM TRIS PH 7.5, 2 MM SPERMIDINE, 1 MM TCEP, 0.01MM ZNCL2 , 90 MM LISO4, 18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.65 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.063 α = 90 b = 112.692 β = 90 c = 132.882 γ = 90
Symmetry Space Group P 21 21 21
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 2009-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.05 40.93 99.9 0.15 10.73 5.9 41439 1.5
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 2.05 2.12 99.3 1.18 1.5 4.7
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 1XC8 2.05 40.93 39352 2103 99.8 0.21507 0.21378 0.2049 0.23885 0.2358 RANDOM 30.072
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] 1.23 -1.52 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.243 r_dihedral_angle_4_deg 16.598 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_1_deg 5.778 r_angle_refined_deg 1.821 r_angle_other_deg 1.288 r_scbond_it 1.23 r_mcangle_it 1.176 r_mcbond_it 0.824 r_mcbond_other 0.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.243 r_dihedral_angle_4_deg 16.598 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_1_deg 5.778 r_angle_refined_deg 1.821 r_angle_other_deg 1.288 r_scbond_it 1.23 r_mcangle_it 1.176 r_mcbond_it 0.824 r_mcbond_other 0.823 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it 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 4289 Nucleic Acid Atoms 569 Solvent Atoms 135 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing