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The crystal structure of E. coli dihydroorotase complexed with 5-fluoroorotic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGE PDB entry 1XGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 15-20% PEG 3350, 0.1M MES, 75mM MgCl2, 150mM KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.515 α = 90 b = 79.708 β = 90 c = 180.611 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2003-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.2 40 94.7 0.086 12.8 4.3 38700 36648 2 32.8
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 2.2 2.257 89.6 0.34 3.3 2.8 2394
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Refinement THROUGHOUT PDB entry 1XGE 2.2 40 38700 36648 1838 94.7 0.17359 0.17071 0.1793 0.22694 0.2311 RANDOM 42.044
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] 2.03 2.69 -4.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_4_deg 16.972 r_dihedral_angle_3_deg 14.041 r_scangle_it 9.042 r_scbond_it 7.28 r_dihedral_angle_1_deg 6.48 r_mcangle_it 5.283 r_mcbond_it 4.614 r_mcbond_other 1.53 r_angle_refined_deg 1.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_4_deg 16.972 r_dihedral_angle_3_deg 14.041 r_scangle_it 9.042 r_scbond_it 7.28 r_dihedral_angle_1_deg 6.48 r_mcangle_it 5.283 r_mcbond_it 4.614 r_mcbond_other 1.53 r_angle_refined_deg 1.357 r_angle_other_deg 0.812 r_symmetry_hbond_refined 0.21 r_nbd_refined 0.207 r_symmetry_vdw_other 0.193 r_nbd_other 0.18 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.141 r_symmetry_vdw_refined 0.095 r_metal_ion_refined 0.09 r_nbtor_other 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5339 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling