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Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two magnesium ions
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% PEG 3,350, 0.2 M NACL
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.924 α = 90 b = 89.924 β = 90 c = 125.577 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 DECTRIS HYBRID PHOTON 2014-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 1.82 48.88 98.8 0.07 14.91 9.7 50673 -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 1.82 1.93 96.9 0.94 2.18 9.06
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 SAD THROUGHOUT NONE 1.82 48.88 47520 2518 97.68 0.15253 0.15053 0.1605 0.18948 0.1979 RANDOM 55.658
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] -0.56 -0.28 -0.56 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_sphericity_free 34.338 r_sphericity_bonded 18.983 r_dihedral_angle_4_deg 13.438 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.42 r_mcangle_it 4.248 r_scbond_it 3.792 r_mcbond_other 3.077 r_mcbond_it 3.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_sphericity_free 34.338 r_sphericity_bonded 18.983 r_dihedral_angle_4_deg 13.438 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.42 r_mcangle_it 4.248 r_scbond_it 3.792 r_mcbond_other 3.077 r_mcbond_it 3.076 r_rigid_bond_restr 1.193 r_angle_refined_deg 1.149 r_angle_other_deg 0.87 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 3385 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling SHELXD phasing SHARP phasing RESOLVE phasing PHENIX phasing