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Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine triphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H5R PDB entry 1H5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M sodium cacodylate, 2.0M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.947 α = 90 b = 91.947 β = 90 c = 69.948 γ = 90
Symmetry Space Group P 42 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 110 CCD ADSC QUANTUM 315r mirrors 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 1.8 30 99.1 0.046 19.3 11.8 28134
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 1.8 1.86 99.3 0.34 12 2735
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 PDB entry 1H5R 1.8 30 28029 1417 98.87 0.1876 0.1856 0.1851 0.2263 0.2256 RANDOM 28.0121
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] 0.21 0.21 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.1 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_3_deg 15.079 r_dihedral_angle_1_deg 6.828 r_scangle_it 5.942 r_scbond_it 3.827 r_mcangle_it 2.535 r_mcbond_it 1.535 r_angle_refined_deg 1.478 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.1 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_3_deg 15.079 r_dihedral_angle_1_deg 6.828 r_scangle_it 5.942 r_scbond_it 3.827 r_mcangle_it 2.535 r_mcbond_it 1.535 r_angle_refined_deg 1.478 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2256 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 68
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing