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Sulfur binding domain of SprMcrA complexed with phosphorothioated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 Ammonium acetate, BIS-TRIS pH5.5, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.94 α = 107.04 b = 48.94 β = 109.79 c = 56.19 γ = 97.26
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 6M 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97776 SSRF BL18U1
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 2.42 28.63 80.2 0.086 0.101 0.053 0.996 10.2 3.5 13319 37.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.51 85 0.628 0.74 0.389 0.685 3.5
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 THROUGHOUT 5ZMO 2.42 28.626 1.97 13317 749 80.24 0.2037 0.2011 0.2015 0.249 0.2502 47.7966
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 17.399 f_angle_d 1.034 f_chiral_restr 0.058 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2613 Nucleic Acid Atoms 808 Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing