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Crystal Structure of Thiamin pyrophosphokinase from Geobacillus thermodenitrificans, Northeast Structural Genomics Consortium Target GtR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 4.2 293 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Na-citrate, 0.1M (NH4)2HPO4, 20% PEG 4000, microbatch under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.422 α = 90 b = 73.652 β = 90 c = 82.657 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 QUANTUM 270 Si(111) 2009-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9787 NSLS X6A
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 2.1 30 99.6 0.092 15.5 3.7 46746 -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 2.1 2.18 100 0.419 3.85 3.7
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD 2.101 26.353 1.35 24867 1264 99.67 0.1802 0.1769 0.1705 0.2417 0.2328 35.767
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.407 f_angle_d 1.077 f_chiral_restr 0.065 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3392 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing REFMAC refinement