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Escherichia coli YtfE_E159L(MN)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 Tris-HCl pH 8.5, PEG 4000, magnesium chloride, manganese chloride
Crystal Properties Matthews coefficient Solvent content 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.824 α = 90 b = 49.671 β = 100.481 c = 88.091 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 S 6M 2017-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976247 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.86 53.39 99.3 0.048 0.058 0.031 0.99 13 3.3 43000 30.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.88 0.787
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5FNN 1.86 53.39 1.34 42989 2089 99.24 0.1821 0.181 0.186 0.2047 0.2073 51.43
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.5586 f_angle_d 0.7902 f_chiral_restr 0.0441 f_bond_d 0.0076 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3460 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Coot model building PHASER phasing XDS data scaling