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Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 6% PEG 3000, 25 mM ZnCl2, 100 mM sodium acetate (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.102 α = 90 b = 57.102 β = 90 c = 368.957 γ = 120
Symmetry Space Group P 32 2 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 ADSC QUANTUM 4 2004-09-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.9796, 1.020, 0.9798 ALS 8.3.1
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 50 99.5 0.082 18.8 5.3 28934 28772 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 96.2 0.35 2.9 3.2 5147
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 (All) 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 MAD THROUGHOUT 2.4 50 28934 28487 1453 99.09 0.195 0.195 0.192 0.1866 0.248 0.2453 RANDOM 36.715
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] 1.01 0.51 1.01 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.015 r_dihedral_angle_4_deg 19.204 r_dihedral_angle_3_deg 18.654 r_dihedral_angle_1_deg 6.814 r_mcangle_it 3.715 r_scangle_it 3.07 r_mcbond_it 2.497 r_scbond_it 2.281 r_angle_refined_deg 1.6 r_symmetry_hbond_refined 0.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.015 r_dihedral_angle_4_deg 19.204 r_dihedral_angle_3_deg 18.654 r_dihedral_angle_1_deg 6.814 r_mcangle_it 3.715 r_scangle_it 3.07 r_mcbond_it 2.497 r_scbond_it 2.281 r_angle_refined_deg 1.6 r_symmetry_hbond_refined 0.352 r_nbtor_refined 0.311 r_metal_ion_refined 0.309 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.213 r_symmetry_metal_ion_refined 0.137 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4777 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 9
Software Software Software Name Purpose Blu-Ice data collection HKL-2000 data reduction SOLVE phasing REFMAC refinement HKL-2000 data scaling