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High-resolution structure of DHDPS from Clostridium botulinum in complex with pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 200mM NaCl, 20%(w/v) PEG 3350, pH 8, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.358 α = 90 b = 54.836 β = 126.29 c = 94.304 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 110 CCD ADSC QUANTUM 210r 2009-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9536 Australian Synchrotron MX1
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 1.19 25.79 99.9 0.069 13.6 5.1 188454 188454 1
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 1.19 1.25 99.9 0.512 2.8 5 27400
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BI8 1.19 25.79 184727 3773 100 0.1129 0.11234 0.13985 0.15 RANDOM 10.724
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] -0.22 -0.14 0.24 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.308 r_dihedral_angle_4_deg 16.706 r_dihedral_angle_3_deg 10.996 r_scangle_it 7.719 r_dihedral_angle_1_deg 6.166 r_scbond_it 5.271 r_mcangle_it 3.084 r_mcbond_it 2.265 r_rigid_bond_restr 2.19 r_angle_refined_deg 2.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.308 r_dihedral_angle_4_deg 16.706 r_dihedral_angle_3_deg 10.996 r_scangle_it 7.719 r_dihedral_angle_1_deg 6.166 r_scbond_it 5.271 r_mcangle_it 3.084 r_mcbond_it 2.265 r_rigid_bond_restr 2.19 r_angle_refined_deg 2.076 r_angle_other_deg 1.425 r_mcbond_other 1.003 r_chiral_restr 0.148 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.001 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 4403 Nucleic Acid Atoms Solvent Atoms 1007 Heterogen Atoms 12
Software Software Software Name Purpose PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling