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Complex structure of AtYchF1 with ppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EE0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 277 PEG
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.46 α = 90 b = 111.5 β = 90 c = 52.33 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 PIXEL DECTRIS PILATUS 2M 2019-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.9792 SSRF BL17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.07 50.01 99.9 0.073 0.028 18.8 13 26569
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.12 0.392
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 5EE0 2.07 50.005 26522 1367 99.853 0.207 0.2056 0.2129 0.2355 0.237 48.867
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] -2.63 -0.066 2.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.32 r_dihedral_angle_4_deg 18.727 r_dihedral_angle_3_deg 13.223 r_lrange_it 6.851 r_lrange_other 6.828 r_dihedral_angle_1_deg 6.521 r_scangle_it 5.618 r_scangle_other 5.618 r_mcangle_it 4.339 r_mcangle_other 4.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.32 r_dihedral_angle_4_deg 18.727 r_dihedral_angle_3_deg 13.223 r_lrange_it 6.851 r_lrange_other 6.828 r_dihedral_angle_1_deg 6.521 r_scangle_it 5.618 r_scangle_other 5.618 r_mcangle_it 4.339 r_mcangle_other 4.338 r_scbond_it 3.675 r_scbond_other 3.673 r_mcbond_it 3.08 r_mcbond_other 3.08 r_angle_refined_deg 1.425 r_angle_other_deg 1.253 r_nbd_refined 0.189 r_nbd_other 0.177 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.158 r_symmetry_nbd_refined 0.15 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2785 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing