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Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMO PDB entry 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; 5% GLYCEROL; SOAKED WITH 10 MM GDP, 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 1.93 36.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.883 α = 90 b = 37.845 β = 101.3 c = 68.839 γ = 90
Symmetry Space Group C 1 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 SBC-3 MIRROR 2008-07-11 M SINGLE WAVELENGTH
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 1.36 50 98.1 0.061 0.061 29.5 3.8 43768 43768 -3 14.7
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 1.36 1.38 86.6 0.386 0.386 2.5 2.8 1884
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 PDB entry 2QMO 1.36 50 41560 41560 2205 97.92 0.13125 0.13125 0.1296 0.1395 0.16171 0.1669 RANDOM 11.494
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] -0.7 -0.71 0.13 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.234 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 11.412 r_dihedral_angle_1_deg 6.181 r_scangle_it 5.528 r_scbond_it 4.069 r_angle_other_deg 3.719 r_mcangle_it 2.784 r_rigid_bond_restr 2.3 r_mcbond_other 2.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.234 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 11.412 r_dihedral_angle_1_deg 6.181 r_scangle_it 5.528 r_scbond_it 4.069 r_angle_other_deg 3.719 r_mcangle_it 2.784 r_rigid_bond_restr 2.3 r_mcbond_other 2.281 r_mcbond_it 2.045 r_angle_refined_deg 1.683 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1744 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 76
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MOLREP phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling