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The structure of UdgX in complex with uracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 0.05M MES pH 5.6, 2.45M (NH4)2SO4 and 0.1M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.05 40.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.407 α = 90 b = 51.448 β = 105.48 c = 55.43 γ = 90
Symmetry Space Group P 1 21 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 OXFORD ONYX CCD 2018-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.15 24.65 98.4 0.066 0.996 9.9 2.3 10655 4.3
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 2.15 2.21 97.1 0.15 0.869 4.3 1.4
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 6IO9 2.15 24.65 10151 500 98.02 0.16529 0.16288 0.1706 0.21211 0.2169 RANDOM 12.852
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] 0.08 0.15 -0.42 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.333 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_3_deg 13.715 r_dihedral_angle_1_deg 6.352 r_long_range_B_other 4.634 r_long_range_B_refined 4.588 r_scangle_other 2.93 r_mcangle_it 2.261 r_mcangle_other 2.261 r_angle_refined_deg 2.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.333 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_3_deg 13.715 r_dihedral_angle_1_deg 6.352 r_long_range_B_other 4.634 r_long_range_B_refined 4.588 r_scangle_other 2.93 r_mcangle_it 2.261 r_mcangle_other 2.261 r_angle_refined_deg 2.116 r_angle_other_deg 1.922 r_scbond_it 1.85 r_scbond_other 1.836 r_mcbond_other 1.366 r_mcbond_it 1.365 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_other 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.007 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 1518 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling PHASER phasing