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Crystal structure of E. coli dihydrouridine synthase C (DusC) (selenomethionine derivative)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 MOLECULAR DIMENSIONS MORPHEUS SCREEN CONDITION D3, pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.8 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.14 α = 90 b = 94.14 β = 90 c = 119.68 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC CCD 2010-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 59.8 99.9 0.12 12.2 7.7 17124 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 100 0.843 2.2 7.9
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 SAD THROUGHOUT NONE 2.6 58.17 16226 860 99.64 0.17858 0.17668 0.1914 0.21447 0.2246 RANDOM 53.164
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] 0.91 0.91 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.194 r_dihedral_angle_4_deg 19.832 r_dihedral_angle_3_deg 14.521 r_dihedral_angle_1_deg 6.274 r_scangle_it 3.067 r_mcangle_it 2.308 r_scbond_it 1.883 r_mcbond_it 1.456 r_mcbond_other 1.456 r_angle_refined_deg 1.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.194 r_dihedral_angle_4_deg 19.832 r_dihedral_angle_3_deg 14.521 r_dihedral_angle_1_deg 6.274 r_scangle_it 3.067 r_mcangle_it 2.308 r_scbond_it 1.883 r_mcbond_it 1.456 r_mcbond_other 1.456 r_angle_refined_deg 1.431 r_angle_other_deg 0.777 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2495 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 31
Software Software Software Name Purpose BUCCANEER model building SCALA data scaling SHELXCD phasing PHASER phasing PARROT phasing BUCCANEER phasing REFMAC refinement