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Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP
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; 150 MM NH4NO3; 100 MM, BIS-TRIS; SOAKED WITH 10 MM GTP, 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 1.92 36.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.151 α = 90 b = 37.504 β = 101.23 c = 69.095 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 1.38 50 98.6 0.05 0.05 35.8 3.9 42504 42504 -3 18.5
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 1.38 1.4 90.4 0.4 0.4 2.2 3.1 1929
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 1.38 50 40040 40040 2142 98.7 0.15991 0.15991 0.15883 0.1623 0.17954 0.183 RANDOM 18.199
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] 0.02 -0.38 0.04 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.814 r_dihedral_angle_4_deg 21.008 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_1_deg 6.334 r_scangle_it 4.373 r_scbond_it 2.815 r_angle_other_deg 2.297 r_angle_refined_deg 1.9 r_mcangle_it 1.808 r_mcbond_it 1.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.814 r_dihedral_angle_4_deg 21.008 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_1_deg 6.334 r_scangle_it 4.373 r_scbond_it 2.815 r_angle_other_deg 2.297 r_angle_refined_deg 1.9 r_mcangle_it 1.808 r_mcbond_it 1.077 r_mcbond_other 0.209 r_chiral_restr 0.127 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_bond_other_d 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 1756 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 63
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