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The structure of a DegV family protein from Eubacterium eligens.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 0.2M sodium acetate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.445 α = 90 b = 57.445 β = 90 c = 186.558 γ = 90
Symmetry Space Group P 41 21 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 QUANTUM 315 2008-10-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97942,0.97929 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 1.8 50 99.9 0.132 19.873 7.7 30039 30039 -3 19.1
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 1.8 1.83 100 0.804 7.8 1451
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 1.8 48.91 29849 29849 1512 99.49 0.162 0.162 0.16 0.1686 0.191 0.204 RANDOM 15.938
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] -0.08 -0.08 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.853 r_dihedral_angle_4_deg 15.538 r_dihedral_angle_3_deg 14.955 r_dihedral_angle_1_deg 5.665 r_scangle_it 4.364 r_scbond_it 2.84 r_mcangle_it 1.452 r_angle_refined_deg 1.374 r_angle_other_deg 0.87 r_mcbond_it 0.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.853 r_dihedral_angle_4_deg 15.538 r_dihedral_angle_3_deg 14.955 r_dihedral_angle_1_deg 5.665 r_scangle_it 4.364 r_scbond_it 2.84 r_mcangle_it 1.452 r_angle_refined_deg 1.374 r_angle_other_deg 0.87 r_mcbond_it 0.734 r_mcbond_other 0.214 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2099 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 41
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