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Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP
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 15% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; SOAKED WITH 10 MM ANP, 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 36.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.085 α = 90 b = 37.582 β = 101.28 c = 69.232 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 1.35 50 97.7 0.035 0.035 46.8 3.8 44773 44773 -3 13.7
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 1.35 1.37 83.8 0.108 0.108 10.5 2.7 1906
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2QMO 1.35 50 42490 42490 2261 97.72 0.14443 0.14443 0.14338 0.16519 0.2144 RANDOM 14.605
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] 0.2 -0.34 -0.22 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_3_deg 11.277 r_dihedral_angle_1_deg 5.956 r_scangle_it 3.777 r_scbond_it 2.621 r_angle_other_deg 2.288 r_angle_refined_deg 1.834 r_mcangle_it 1.659 r_mcbond_it 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_3_deg 11.277 r_dihedral_angle_1_deg 5.956 r_scangle_it 3.777 r_scbond_it 2.621 r_angle_other_deg 2.288 r_angle_refined_deg 1.834 r_mcangle_it 1.659 r_mcbond_it 0.96 r_mcbond_other 0.186 r_chiral_restr 0.123 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 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 1750 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 80
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