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crystal structure of biotin ligase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HXD PDB ENTRY 1HXD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1M TRIS HCL PH8.5, 0.2M TRIMETHYLAMINE N-OXIDE, 20%(W/V) MPEG 2000, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.3 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.099 α = 90 b = 81.007 β = 90 c = 101.881 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 MARRESEARCH MIRROR 2005-05-09 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 1.8 39.38 99.8 0.04 36.3 16 48344 29
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 1.8 1.9 99.9 0.56 3.9 8.5
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 1HXD 1.8 39.37 45951 2326 100 0.187 0.185 0.1942 0.224 0.2274 THIN SHELLS 28.69
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] -0.77 1.48 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.377 r_dihedral_angle_4_deg 19.492 r_dihedral_angle_3_deg 14.005 r_dihedral_angle_1_deg 10.836 r_scangle_it 3.937 r_scbond_it 2.59 r_angle_refined_deg 1.775 r_mcangle_it 1.659 r_mcbond_it 1.178 r_angle_other_deg 0.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.377 r_dihedral_angle_4_deg 19.492 r_dihedral_angle_3_deg 14.005 r_dihedral_angle_1_deg 10.836 r_scangle_it 3.937 r_scbond_it 2.59 r_angle_refined_deg 1.775 r_mcangle_it 1.659 r_mcbond_it 1.178 r_angle_other_deg 0.903 r_symmetry_vdw_other 0.334 r_nbd_refined 0.217 r_nbd_other 0.197 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.126 r_chiral_restr 0.107 r_nbtor_other 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 3503 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CaspR phasing