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Crystal structure of SdeA catalytic core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other It was solved by MR on a crude model from experimental phasing experiment (data not deposited)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 300 100mM Bis Tris Propane pH 7.0-8.0, 0.1-0.2M sodium citrate tribasic dihydrate, 20-30% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.93 58.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.721 α = 90 b = 80.824 β = 110.57 c = 86.518 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 100 PIXEL DECTRIS PILATUS 2M 2017-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
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 2.802 44.216 99.6 0.139 13.03 6.8 43693
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.802 2.902
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE It was solved by MR on a crude model from experimental phasing experiment (data not deposited) 2.802 44.216 1.2 43693 2199 99.17 0.2597 0.2578 0.2932 0.2602
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 14.518 f_angle_d 0.505 f_chiral_restr 0.038 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4838 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing