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Putative antitoxin component, CHU_2935 protein, from Xre family from Prevotella buccae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 2 M ammonium sulfate, 0.1 M phosphate citrate-buffer, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.855 α = 90 b = 44.882 β = 90 c = 86.408 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 2007-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 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 1.65 39.8 100 0.098 7.1 11.5 19302 19302 24.7
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) 1.65 1.68 100 0.895 2.74 10.2 952
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3BS3 1.65 39.8 19239 19239 986 99.79 0.1384 0.1384 0.1356 0.1477 0.1919 0.1988 RANDOM 16.7633
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] 0.01 0.36 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_3_deg 11.8 r_dihedral_angle_4_deg 10.318 r_scangle_it 5.935 r_dihedral_angle_1_deg 4.647 r_scbond_it 3.996 r_mcangle_it 2.507 r_mcbond_it 1.601 r_rigid_bond_restr 1.593 r_angle_refined_deg 1.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_3_deg 11.8 r_dihedral_angle_4_deg 10.318 r_scangle_it 5.935 r_dihedral_angle_1_deg 4.647 r_scbond_it 3.996 r_mcangle_it 2.507 r_mcbond_it 1.601 r_rigid_bond_restr 1.593 r_angle_refined_deg 1.432 r_angle_other_deg 0.968 r_mcbond_other 0.524 r_chiral_restr 0.097 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1087 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing