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Structure of sponge-phase grown PepTst2 collected by rotation serial crystallography on a COC membrane at a synchrotron source
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XNJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 325 mM NH4H2PO4, 100 mM HEPES pH 7.0, 21-22%(v/v) PEG 400 and 10 mM dipeptide, AF
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.76 α = 90 b = 110.23 β = 90 c = 109.82 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 16M 2019-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3 49.26 94.7 0.974 3.84 3.05 12579 70.78
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 3 3.08 0.217 0.78
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 4XNJ 3 49.26 1.35 12579 627 99.25 0.2421 0.2398 0.2399 0.2869 0.2839 67.33
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 18.9167 f_angle_d 0.4932 f_chiral_restr 0.0362 f_plane_restr 0.0035 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3957 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing