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Crystal structure of a putative DNA-binding protein from Bacteroides fragilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1M Tris-HCl pH 8.5, 0.2M LiSO4, 1.25M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.337 α = 90 b = 63.337 β = 90 c = 34.706 γ = 120
Symmetry Space Group P 31 2 1
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 2007-11-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931, 0.97945 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 50 98 0.094 9.2 11.9 9728 9728 -3 26.1
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 1.65 1.69 98 0.509 2.9 10 632
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 MAD THROUGHOUT 1.65 29.32 9714 9714 463 98.02 0.185 0.185 0.183 0.182 0.219 0.2156 RANDOM 32.059
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] -1.1 -0.55 -1.1 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.062 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_3_deg 14.635 r_dihedral_angle_1_deg 4.079 r_scangle_it 3.348 r_scbond_it 2.266 r_mcangle_it 1.355 r_angle_refined_deg 1.346 r_mcbond_it 0.989 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.062 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_3_deg 14.635 r_dihedral_angle_1_deg 4.079 r_scangle_it 3.348 r_scbond_it 2.266 r_mcangle_it 1.355 r_angle_refined_deg 1.346 r_mcbond_it 0.989 r_nbtor_refined 0.305 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 502 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building