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Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G4T pdb entry 1G4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 modified microbatch 4.6 291 30%v/v PEG 2000 MME, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, modified microbatch, temperature 291KK
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.386 α = 90 b = 81.21 β = 90 c = 152.903 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 100 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.7 30 100 0.098 50284
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) 1.7 1.76 100 0.281
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-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 1G4T 1.7 29.086 50281 1540 100 0.189 0.18878 0.188 0.1999 0.2147 0.2282 thin shells 16.981
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] 0.012 0.004 -0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.796 r_dihedral_angle_4_deg 13.605 r_dihedral_angle_3_deg 11.622 r_dihedral_angle_1_deg 5.348 r_scangle_it 4.355 r_mcangle_it 3.09 r_scbond_it 2.965 r_mcbond_it 2.603 r_mcangle_other 1.873 r_scangle_other 1.824
Show All KeysRMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.796 r_dihedral_angle_4_deg 13.605 r_dihedral_angle_3_deg 11.622 r_dihedral_angle_1_deg 5.348 r_scangle_it 4.355 r_mcangle_it 3.09 r_scbond_it 2.965 r_mcbond_it 2.603 r_mcangle_other 1.873 r_scangle_other 1.824 r_angle_refined_deg 1.367 r_scbond_other 0.889 r_angle_other_deg 0.831 r_mcbond_other 0.672 r_symmetry_vdw_refined 0.336 r_symmetry_vdw_other 0.311 r_nbd_refined 0.218 r_nbd_other 0.186 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.081 r_nbtor_other 0.081 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Hide All KeysNon-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3049 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection AMoRE phasing