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Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two manganese ions.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% PEG 3,350, 0.2 M NACL
Crystal Properties Matthews coefficient Solvent content 2.99 58.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.676 α = 90 b = 89.676 β = 90 c = 125.329 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2014-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999990, 1.700020 SLS X10SA
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 1.5 48.77 99.8 0.04 26.35 15.48 91340 -3
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 1.5 1.59 99.1 1.34 2.03 14.18
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 OTHER THROUGHOUT NONE 1.5 48.77 86573 4513 100 0.15242 0.15145 0.1611 0.17087 0.18 RANDOM 52.368
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] 0.38 0.19 0.38 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_sphericity_free 26.526 r_sphericity_bonded 14.418 r_dihedral_angle_4_deg 12.377 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 5.384 r_mcangle_it 3.123 r_scbond_it 3.077 r_mcbond_it 2.384 r_mcbond_other 2.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_sphericity_free 26.526 r_sphericity_bonded 14.418 r_dihedral_angle_4_deg 12.377 r_dihedral_angle_3_deg 11.835 r_dihedral_angle_1_deg 5.384 r_mcangle_it 3.123 r_scbond_it 3.077 r_mcbond_it 2.384 r_mcbond_other 2.382 r_angle_refined_deg 1.186 r_angle_other_deg 0.87 r_rigid_bond_restr 0.814 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3381 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling