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Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus
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 7 293 0.1M Tris, 1.9M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.03 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.526 α = 90 b = 88.704 β = 90 c = 129.39 γ = 90
Symmetry Space Group I 2 2 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 1.9 30 98.82 0.051 9.4 31598 31533
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 1.9 1.97 93.3 0.335 8.3
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 1.9 30 31533 1593 98.82 0.2191 0.217 0.215 0.2589 0.2572 RANDOM 44.7551
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] 3.53 -0.6 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.252 r_dihedral_angle_4_deg 22.83 r_dihedral_angle_3_deg 19.423 r_dihedral_angle_1_deg 7.393 r_mcangle_it 2.9 r_mcbond_it 1.776 r_angle_refined_deg 1.506 r_chiral_restr 0.141 r_bond_refined_d 0.02 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.252 r_dihedral_angle_4_deg 22.83 r_dihedral_angle_3_deg 19.423 r_dihedral_angle_1_deg 7.393 r_mcangle_it 2.9 r_mcbond_it 1.776 r_angle_refined_deg 1.506 r_chiral_restr 0.141 r_bond_refined_d 0.02 r_gen_planes_refined 0.014 r_scbond_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2234 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling MOLREP phasing