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Streptomyces PAC13 (Y89F) with uridine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M ammonium fluoride, 20 % w/v PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.792 α = 90 b = 66.792 β = 90 c = 54.56 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN A200 2016-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 1.6 57.84 95.3 0.998 37.3 3.3 17880
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 1.6 1.71 76.8 0.858 7.6 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 57.84 16947 847 94.61 0.15932 0.15809 0.172 0.18537 0.2001 RANDOM 15.146
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] -0.18 -0.09 -0.18 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.919 r_dihedral_angle_4_deg 13.991 r_dihedral_angle_1_deg 13.904 r_dihedral_angle_3_deg 11.533 r_long_range_B_refined 5.871 r_long_range_B_other 5.868 r_scangle_other 2.783 r_scbond_it 1.712 r_scbond_other 1.712 r_mcangle_it 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.919 r_dihedral_angle_4_deg 13.991 r_dihedral_angle_1_deg 13.904 r_dihedral_angle_3_deg 11.533 r_long_range_B_refined 5.871 r_long_range_B_other 5.868 r_scangle_other 2.783 r_scbond_it 1.712 r_scbond_other 1.712 r_mcangle_it 1.47 r_mcangle_other 1.469 r_angle_refined_deg 1.255 r_mcbond_it 0.867 r_mcbond_other 0.863 r_angle_other_deg 0.737 r_chiral_restr 0.086 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 975 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling