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Crystal structure of E. coli dihydrouridine synthase C (DusC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BF9 PDB ENTRY 4BF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 MOLECULAR DIMENSION MORPHEUS SCREEN CONDITION C10, pH 8.5
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.54 α = 90 b = 99.953 β = 90 c = 119.896 γ = 90
Symmetry Space Group P 21 21 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 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 1.65 60 100 0.1 11 7.3 99677 -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 1.65 1.74 100 0.71 2.6 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4BF9 1.65 51.13 94507 5013 99.91 0.13655 0.13443 0.17673 0.1911 RANDOM 26.619
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] -0.88 0.71 0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.306 r_dihedral_angle_2_deg 36.309 r_dihedral_angle_4_deg 16.519 r_sphericity_bonded 14.828 r_dihedral_angle_3_deg 12.056 r_dihedral_angle_1_deg 5.494 r_rigid_bond_restr 3.193 r_angle_refined_deg 1.278 r_angle_other_deg 0.791 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.306 r_dihedral_angle_2_deg 36.309 r_dihedral_angle_4_deg 16.519 r_sphericity_bonded 14.828 r_dihedral_angle_3_deg 12.056 r_dihedral_angle_1_deg 5.494 r_rigid_bond_restr 3.193 r_angle_refined_deg 1.278 r_angle_other_deg 0.791 r_chiral_restr 0.073 r_bond_refined_d 0.009 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4894 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing