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Crystal structure of DctP6, a Bordetella pertussis extracytoplasmic solute receptor binding pyroglutamic acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 36% (w/v) PEG 2000 MME, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.39 α = 90 b = 108.39 β = 90 c = 63.09 γ = 90
Symmetry Space Group P 41 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 CCD MAR CCD 165 mm 2006-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97942 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 19.85 35380 35219
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1.8 19.85 35219 1765 99.66 0.189 0.187 0.1867 0.236 0.2368 RANDOM 22.257
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.563 r_dihedral_angle_4_deg 20.974 r_dihedral_angle_3_deg 15.882 r_dihedral_angle_1_deg 5.919 r_sphericity_free 5.235 r_scangle_it 3.517 r_scbond_it 2.618 r_sphericity_bonded 2.481 r_rigid_bond_restr 1.999 r_mcangle_it 1.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.563 r_dihedral_angle_4_deg 20.974 r_dihedral_angle_3_deg 15.882 r_dihedral_angle_1_deg 5.919 r_sphericity_free 5.235 r_scangle_it 3.517 r_scbond_it 2.618 r_sphericity_bonded 2.481 r_rigid_bond_restr 1.999 r_mcangle_it 1.476 r_angle_refined_deg 1.435 r_mcbond_it 0.99 r_nbtor_refined 0.302 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2349 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction XSCALE data scaling AMoRE phasing