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Crystal structure of Tmm from Myroides profundi D25
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.1 M Magnesium acetate
0.1M Mes, pH 6.5
10%(w/v) PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.48 50.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.543 α = 90 b = 99.372 β = 90 c = 144.925 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2018-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.987 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.686 81.96 93.4 0.082 0.089 0.034 17.8 11.3 115098
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.78 69.9 0.44 0.317 5.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5IPY 1.686 81.956 112983 5727 91.68 0.1788 0.1773 0.1784 0.2059 0.2045 27.91
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] -4.5972 -3.0655 7.6627
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.306 f_angle_d 1.118 f_chiral_restr 0.083 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7374 Nucleic Acid Atoms Solvent Atoms 846 Heterogen Atoms 202
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data scaling PHENIX model building PHENIX phasing