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Crystal structure of the N-terminal peptidase C39 like domain of the toxin secretion ATP-binding protein from Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 289 1.0 M Ammonium citrate (dibasic), 0.1 M Sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.97 37.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.173 α = 90 b = 46.173 β = 90 c = 105.975 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 315 Mirrors 2007-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97930 APS 19-ID
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 1.37 42.33 99 0.061 14.1 16.6 24811 24811 14.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.37 1.42 98.4 0.394 6 14.2 2406
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.37 42.33 22212 22212 2508 99.09 0.158 0.158 0.155 0.1507 0.182 0.1784 RANDOM 18.387
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_3_deg 14.81 r_dihedral_angle_4_deg 12.848 r_sphericity_free 8.776 r_dihedral_angle_1_deg 5.55 r_scangle_it 4.996 r_sphericity_bonded 4.858 r_scbond_it 3.556 r_mcangle_it 2.565 r_rigid_bond_restr 1.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_3_deg 14.81 r_dihedral_angle_4_deg 12.848 r_sphericity_free 8.776 r_dihedral_angle_1_deg 5.55 r_scangle_it 4.996 r_sphericity_bonded 4.858 r_scbond_it 3.556 r_mcangle_it 2.565 r_rigid_bond_restr 1.923 r_mcbond_it 1.897 r_angle_refined_deg 1.662 r_nbtor_refined 0.309 r_nbd_refined 0.301 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.168 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1154 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELX phasing MLPHARE phasing RESOLVE phasing ARP/wARP model building