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TenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UDD PDB ENTRY 1UDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 3 microliters of 10 mg/mL TenA in 20 mM Tris pH8, 20 mM NaCl, mixed with 3 microliters reservoir = 16% PEG 2000MME, and 0.1 M sodium phosphate, pH 6.6., VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.757 α = 90 b = 134.926 β = 90 c = 144.029 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2001-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
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 2.8 90 99.9 0.095 11.6 12.4 27783 27783 76
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 2.9 100 100 0.586
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1UDD 2.8 19.7 22752 22752 1152 82.54 0.234 0.234 0.231 0.23 0.286 0.2789 RANDOM 21.666
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] 2.42 -1.53 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.992 r_dihedral_angle_4_deg 19.466 r_dihedral_angle_3_deg 16.425 r_scangle_it 6.121 r_mcangle_it 5.073 r_scbond_it 4.56 r_mcbond_it 3.702 r_dihedral_angle_1_deg 3.26 r_angle_refined_deg 1.123 r_angle_other_deg 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.992 r_dihedral_angle_4_deg 19.466 r_dihedral_angle_3_deg 16.425 r_scangle_it 6.121 r_mcangle_it 5.073 r_scbond_it 4.56 r_mcbond_it 3.702 r_dihedral_angle_1_deg 3.26 r_angle_refined_deg 1.123 r_angle_other_deg 0.878 r_mcbond_other 0.68 r_symmetry_vdw_refined 0.226 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.218 r_symmetry_vdw_other 0.208 r_nbtor_refined 0.191 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.158 r_nbtor_other 0.085 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_xyhbond_nbd_other 0.005 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6822 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 67
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction