☰ Navigation Tabs
Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed double-strand DNA break.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IRU PDB ENTRY 2IRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 285 20% PEG 3350, 200mM Ammonium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.58 α = 90 b = 80.11 β = 111.62 c = 118.39 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 RIGAKU SATURN 944+ mirrors 2009-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 110.061 98.5 0.117 12.3 6.6 58964 58964 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 96.1 0.825 0.825 0.9 6.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IRU 2.4 37.64 55990 2951 98.1 0.19969 0.19734 0.24529 0.2304 RANDOM 46.065
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] 19.02 -6.55 40.65 -59.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.837 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 17.86 r_dihedral_angle_1_deg 6.164 r_mcangle_it 1.4 r_angle_refined_deg 1.268 r_scbond_it 1.113 r_mcbond_it 0.908 r_chiral_restr 0.081 r_gen_planes_refined 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.837 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 17.86 r_dihedral_angle_1_deg 6.164 r_mcangle_it 1.4 r_angle_refined_deg 1.268 r_scbond_it 1.113 r_mcbond_it 0.908 r_chiral_restr 0.081 r_gen_planes_refined 0.018 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 8680 Nucleic Acid Atoms 1060 Solvent Atoms 196 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection