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Crystal Structure of Thiamin pyrophosphokinase family protein from Enterococcus faecalis, Northeast Structural Genomics Consortium Target EfR150
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other GtR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: MgSO4 - 0.15M, Bis-Tris 0.1M, PEG8K 16%, ATP, MgCl2, thiamine, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.92 57.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.286 α = 90 b = 102.112 β = 98.126 c = 94.277 γ = 90
Symmetry Space Group P 1 21 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 MIRRORS 2010-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97853 NSLS X4C
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 2.788 50 99.8 0.097 7.9 3.1 56964 -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 2.8 2.9 99.8 0.484 1.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MAD FREE R-VALUE GtR2 2.788 48.53 29025 1476 99.17 0.172 0.1679 0.2028 0.2493 0.2641 43.906
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] -1.942 -1.008 -1.031 3.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.498 r_dihedral_angle_6_deg 14.721 r_dihedral_angle_2_deg 11.604 r_dihedral_angle_1_deg 8.948 r_lrange_it 7.762 r_scangle_it 6.055 r_mcangle_it 3.977 r_scbond_it 3.924 r_angle_refined_deg 2.791 r_mcbond_it 2.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.498 r_dihedral_angle_6_deg 14.721 r_dihedral_angle_2_deg 11.604 r_dihedral_angle_1_deg 8.948 r_lrange_it 7.762 r_scangle_it 6.055 r_mcangle_it 3.977 r_scbond_it 3.924 r_angle_refined_deg 2.791 r_mcbond_it 2.453 r_nbtor_refined 0.331 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.257 r_chiral_restr 0.179 r_xyhbond_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6776 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling SHELXD phasing