☰ Navigation Tabs
X-ray structure of Mycobacterium tuberculosis Dodecin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V21 PDB ENTRY 2V21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 10 MM CO CL2, 100 MM NAOAC PH 5.0, 200 MM HEXANEDIOL.
Crystal Properties Matthews coefficient Solvent content 3.18 61.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.302 α = 90 b = 94.302 β = 90 c = 230.907 γ = 120
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 MARRESEARCH MX-300 2007-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 1.7 14.91 99.7 0.05 24.8 11.1 43832 -3 26.7
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 1.7 1.79 100 0.78 3.3 11.1
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 2V21 1.7 14.91 42659 1084 99.76 0.17261 0.17198 0.1819 0.19743 0.1787 RANDOM 27.99
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] -0.3 -0.15 -0.3 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.777 r_dihedral_angle_4_deg 14.867 r_dihedral_angle_3_deg 12.059 r_dihedral_angle_1_deg 6.61 r_scangle_it 3.642 r_scbond_it 2.134 r_mcangle_it 1.504 r_angle_refined_deg 1.342 r_mcbond_it 0.831 r_angle_other_deg 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.777 r_dihedral_angle_4_deg 14.867 r_dihedral_angle_3_deg 12.059 r_dihedral_angle_1_deg 6.61 r_scangle_it 3.642 r_scbond_it 2.134 r_mcangle_it 1.504 r_angle_refined_deg 1.342 r_mcbond_it 0.831 r_angle_other_deg 0.788 r_mcbond_other 0.209 r_chiral_restr 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other 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 2084 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing