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YnDL in Complex with 5 amino acid (PGA) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1M Sodium Acetate, 5% gamma-PGA, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.86 33.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.592 α = 90 b = 47.651 β = 90 c = 99.328 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 PILATUS3 6M 2017-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.00000 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 15.75 99 24.58 1.9 20613 14.34
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 THROUGHOUT 3A9L 1.7 15.75 1.34 20609 1087 99.05 0.169 0.167 0.2035 0.1846
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 16.416 f_angle_d 0.784 f_chiral_restr 0.06 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1581 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing