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Crystal structure of dimeric protein of unknown function and ferredoxin-like fold (YP_212648.1) from Bacteroides fragilis NCTC 9343 at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 NANODROP, 0.2M (NH4)2SO4, 20.0% PEG 3350, No Buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.31 α = 90 b = 72.31 β = 90 c = 233.02 γ = 120
Symmetry Space Group P 61 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-11-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97867 SSRL BL11-1
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 1.85 29.399 99.7 0.09 31933 -3 29.156
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 1.85 1.92 98.6 0.012 1.7
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 1.85 29.399 31830 1612 99.72 0.172 0.17 0.174 0.205 0.2041 RANDOM 32.402
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] 0.58 0.29 0.58 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 14.104 r_dihedral_angle_3_deg 13.028 r_scangle_it 6.465 r_dihedral_angle_1_deg 5.545 r_scbond_it 4.731 r_mcangle_it 2.44 r_mcbond_it 2.08 r_angle_refined_deg 1.468 r_angle_other_deg 0.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.697 r_dihedral_angle_4_deg 14.104 r_dihedral_angle_3_deg 13.028 r_scangle_it 6.465 r_dihedral_angle_1_deg 5.545 r_scbond_it 4.731 r_mcangle_it 2.44 r_mcbond_it 2.08 r_angle_refined_deg 1.468 r_angle_other_deg 0.971 r_mcbond_other 0.508 r_nbd_refined 0.212 r_nbd_other 0.199 r_symmetry_hbond_refined 0.186 r_symmetry_vdw_other 0.185 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.148 r_chiral_restr 0.093 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1646 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXCD phasing autoSHARP phasing