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Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 285 20% PEG 3350, 0.2 M Mg acetate, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.053 α = 90 b = 75.796 β = 92.68 c = 96.1 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2006-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54180
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 1.65 20.37 90.1 0.07 0.029 23.7 6.4 63571 -3.7 20.1
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 1.65 1.74 74.8 0.235 0.129 3 3.6 7663
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 (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 1.65 20.37 63550 60313 3237 89.86 0.19273 0.1902 0.1853 0.23896 0.2342 RANDOM 15.758
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] 0.65 -0.12 -0.21 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.814 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 13.589 r_dihedral_angle_1_deg 6.097 r_scangle_it 3.382 r_scbond_it 2.269 r_angle_refined_deg 1.478 r_mcangle_it 1.43 r_mcbond_it 0.924 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.814 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 13.589 r_dihedral_angle_1_deg 6.097 r_scangle_it 3.382 r_scbond_it 2.269 r_angle_refined_deg 1.478 r_mcangle_it 1.43 r_mcbond_it 0.924 r_nbtor_refined 0.302 r_xyhbond_nbd_refined 0.26 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.198 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4344 Nucleic Acid Atoms Solvent Atoms 663 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling PHASER phasing