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Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with dGTP and Manganese.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 285 0.1M Na Hepes, 0.01M MnCl2, 10%(v/v) iso-propanol, 20% PEG 4000, 0.01M dGTP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.221 α = 90 b = 75.87 β = 92.59 c = 95.809 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 2006-07-16 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 1.78 40.49 100 0.07 0.095 15.5 3.7 56549 -3.7 20.26114
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 1.78 1.88 99.9 0.175 0.237 4.3 3.6 8240
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 1.78 40.49 56528 53660 2868 99.96 0.18453 0.18206 0.1795 0.23034 0.226 RANDOM 17.099
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] 0.4 -0.17 -0.2 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 5.987 r_scangle_it 3.191 r_scbond_it 2.098 r_angle_refined_deg 1.414 r_mcangle_it 1.254 r_mcbond_it 0.794 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.396 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 5.987 r_scangle_it 3.191 r_scbond_it 2.098 r_angle_refined_deg 1.414 r_mcangle_it 1.254 r_mcbond_it 0.794 r_nbtor_refined 0.3 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.206 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.095 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4362 Nucleic Acid Atoms Solvent Atoms 659 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling PHASER phasing