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Crystal structure of Uracil phosphoribosyltransferase (TM0721) from Thermotoga maritima at 2.30 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 9 277 2.4M ammonium sulfate, 0.1M bicine pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.078 α = 90 b = 87.406 β = 115.29 c = 90.826 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 4 bent conical Si-mirror (Rh coating) 2003-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 50 100 0.102 10.16 3.72 41796 41796 51.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.71 0.752 1.49 3.66 4138
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 1i5e 2.3 30.93 39885 2126 99.68 0.17004 0.16658 0.1795 0.23635 0.2415 RANDOM 45.165
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] -0.39 -0.13 0.53 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.392 r_dihedral_angle_4_deg 17.785 r_dihedral_angle_3_deg 17.403 r_dihedral_angle_1_deg 6.566 r_scangle_it 3.466 r_scbond_it 2.216 r_angle_refined_deg 1.702 r_mcangle_it 1.39 r_mcbond_it 0.966 r_angle_other_deg 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.392 r_dihedral_angle_4_deg 17.785 r_dihedral_angle_3_deg 17.403 r_dihedral_angle_1_deg 6.566 r_scangle_it 3.466 r_scbond_it 2.216 r_angle_refined_deg 1.702 r_mcangle_it 1.39 r_mcbond_it 0.966 r_angle_other_deg 0.915 r_symmetry_hbond_refined 0.196 r_nbd_refined 0.19 r_nbd_other 0.188 r_xyhbond_nbd_refined 0.184 r_symmetry_vdw_refined 0.175 r_symmetry_vdw_other 0.17 r_chiral_restr 0.096 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6554 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 129
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement