☰ Navigation Tabs
Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 20% PEG3350; 100 MM NH4NO3; 100 MM, BIS-TRIS; 10 MM ATP; 10 MM MGCL2; 10 MM 8-AMINOOCTANOIC ACID; IN SITU
PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.773 α = 90 b = 131.905 β = 90 c = 133.099 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 MIRROR 2008-07-09 M MOLECULAR REPLACEMENT
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM
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 2.8 50 99.9 0.099 0.099 21.615 7.7 35576 35576 -3 81.3
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 2.8 2.85 100 0.846 0.846 2 7.9 1765
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2QMO 2.8 50 35281 35281 1765 99.92 0.204 0.204 0.201 0.2193 0.246 0.2645 RANDOM 59.69
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] -1.37 2.76 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.917 r_dihedral_angle_4_deg 22.741 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_1_deg 5.231 r_scangle_it 3.98 r_scbond_it 2.714 r_mcangle_it 2.107 r_mcbond_it 1.368 r_angle_refined_deg 1.356 r_angle_other_deg 1.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.917 r_dihedral_angle_4_deg 22.741 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_1_deg 5.231 r_scangle_it 3.98 r_scbond_it 2.714 r_mcangle_it 2.107 r_mcbond_it 1.368 r_angle_refined_deg 1.356 r_angle_other_deg 1.149 r_mcbond_other 0.27 r_chiral_restr 0.063 r_bond_refined_d 0.014 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10345 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 289
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement Coot model building HKL-3000 phasing HKL-2000 data reduction HKL-2000 data scaling