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Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 277 2.0M (NH4)2SO4, 2.0% PEG-400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.75 66.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.03 α = 90 b = 107.03 β = 90 c = 207.26 γ = 120
Symmetry Space Group P 6 2 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 2004-09-18 M SINGLE WAVELENGTH 2 1 x-ray M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1 2 SYNCHROTRON ALS BEAMLINE 8.3.1 0.979694,0.979811,1.020035 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2 2.4 29.02 99.9 0.13 18 11.7 28264 42.73
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) 1,2 2.4 2.53 100 0.616 3.6 6.8 4033
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 MAD THROUGHOUT 2.4 29.02 26875 1388 99.88 0.20473 0.20268 0.2051 0.2444 0.2439 RANDOM 32.774
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] 1.31 0.66 1.31 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.728 r_dihedral_angle_4_deg 17.055 r_dihedral_angle_3_deg 16.045 r_scangle_it 11.232 r_scbond_it 7.925 r_dihedral_angle_1_deg 4.946 r_mcangle_it 3.852 r_mcbond_it 2.903 r_angle_refined_deg 1.605 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.728 r_dihedral_angle_4_deg 17.055 r_dihedral_angle_3_deg 16.045 r_scangle_it 11.232 r_scbond_it 7.925 r_dihedral_angle_1_deg 4.946 r_mcangle_it 3.852 r_mcbond_it 2.903 r_angle_refined_deg 1.605 r_nbtor_refined 0.293 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3129 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHELX model building autoSHARP phasing REFMAC refinement CCP4 data scaling SHELX phasing