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Crystal structure of ATP-grasp ligase PruB from Streptomyces coelicolor A3(2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, and 10% (v/v) 1,4-dioxane
Crystal Properties Matthews coefficient Solvent content 3.7 71.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 222.04 α = 90 b = 222.04 β = 90 c = 87.007 γ = 90
Symmetry Space Group I 4 2 2
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 EIGER X 16M 2021-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 2.91 49.65 99.47 0.04394 0.06214 0.04394 0.996 8.86 2 24070 74.47
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 2.91 3.014 97.38 0.3514 0.497 0.3514 0.683 1.59 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.91 49.65 1.34 24040 1201 99.47 0.2099 0.2073 0.209 0.2582 0.2615 69.08
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 7.2362 f_angle_d 1.4335 f_chiral_restr 0.0617 f_plane_restr 0.0201 f_bond_d 0.0134
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4391 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing