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Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA
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%(w/v)PEG 3350, 0.2 M Ammonium chloride, 10mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.58 52.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.531 α = 90 b = 111.788 β = 90 c = 139.542 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 ADSC QUANTUM 210 2006-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.98400 ESRF BM16
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 2.4 30 96.8 0.063 9.1 6.8 29540
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 2.4 2.49 98.1 0.391 6.5 2938
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 2IRU 2.4 21.124 29486 1502 96.78 0.229 0.227 0.2309 0.272 0.274 RANDOM 90.14
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] 4.77 -7.02 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.146 r_dihedral_angle_4_deg 15.472 r_dihedral_angle_3_deg 14.56 r_dihedral_angle_1_deg 5.572 r_scangle_it 2.173 r_scbond_it 1.576 r_mcangle_it 1.048 r_angle_refined_deg 1.015 r_mcbond_it 0.681 r_symmetry_hbond_refined 0.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.146 r_dihedral_angle_4_deg 15.472 r_dihedral_angle_3_deg 14.56 r_dihedral_angle_1_deg 5.572 r_scangle_it 2.173 r_scbond_it 1.576 r_mcangle_it 1.048 r_angle_refined_deg 1.015 r_mcbond_it 0.681 r_symmetry_hbond_refined 0.472 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4348 Nucleic Acid Atoms 693 Solvent Atoms 97 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction