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PaaK family AMP-ligase with AMP and substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M KSCN, 0.1 M sodium citrate pH 6.0, 30% PEG MME 2K
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.373 α = 90 b = 138.584 β = 90 c = 130.414 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 PILATUS 6M 2018-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 69.29 100 0.06 0.999 13.2 7.1 70886
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 99.6 0.841 0.51 1.4 6.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SIW 1.95 69.29 67170 3684 99.97 0.1883 0.1862 0.1967 0.2287 0.2286 RANDOM 59.112
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] -2.46 1.13 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.59 r_dihedral_angle_4_deg 20.001 r_dihedral_angle_3_deg 13.996 r_dihedral_angle_1_deg 6.982 r_angle_refined_deg 1.455 r_angle_other_deg 1.244 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.59 r_dihedral_angle_4_deg 20.001 r_dihedral_angle_3_deg 13.996 r_dihedral_angle_1_deg 6.982 r_angle_refined_deg 1.455 r_angle_other_deg 1.244 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6773 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing