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Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DD7 PDB ENTRY 3DD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 294 2250 mM NaCl, 100 mM NaH2PO4, 100 mM K2HPO4, 3% ethanol, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.45 64.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.899 α = 90 b = 111.277 β = 90 c = 118.747 γ = 90
Symmetry Space Group P 21 21 21
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 2006-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 2.7 40 91.2 0.138 8.5 8.2 32176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.75 94.4 7.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3DD7 2.71 30 30521 1583 90.9 0.219 0.217 0.2203 0.267 0.2631 RANDOM 55.741
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] -2.13 1.62 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.705 r_dihedral_angle_4_deg 18.025 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 4.379 r_scangle_it 1.481 r_angle_other_deg 1.303 r_angle_refined_deg 0.91 r_scbond_it 0.835 r_mcangle_it 0.618 r_mcbond_it 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.705 r_dihedral_angle_4_deg 18.025 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 4.379 r_scangle_it 1.481 r_angle_other_deg 1.303 r_angle_refined_deg 0.91 r_scbond_it 0.835 r_mcangle_it 0.618 r_mcbond_it 0.326 r_chiral_restr 0.047 r_mcbond_other 0.041 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5984 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling COMO phasing REFMAC refinement PDB_EXTRACT data extraction