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TenA Homolog/Thi-4 Thiaminase complexed with product 4-amino-5-hydroxymethyl-2-methylpyrimidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GM7 PDB ID 2GM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 18 mg/mL protein was complexed with thiamine diphosphate and enzyme mediated catalysis produced 4-amino-5-hydroxymethyl-2-methylpyrimidine.
Reservoir contains 20% PEG 8000, 0.1M Tris pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.647 α = 90 b = 94.287 β = 113.65 c = 73.198 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 315 2005-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00000 ALS 5.0.2
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 2.5 80 99 0.11 13 2.9 32375 32375 53
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 2.5 2.59 98.3 98.3 0.299 2.8
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 ID 2GM7 2.5 67.12 30264 30264 1533 99.08 0.189 0.189 0.187 0.1944 0.237 0.2416 RANDOM 29.708
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] 2.28 1.05 -2.57 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 21.95 r_dihedral_angle_3_deg 17.166 r_scangle_it 10.862 r_scbond_it 9.301 r_mcangle_it 8.085 r_mcbond_it 7.35 r_dihedral_angle_1_deg 3.453 r_mcbond_other 1.962 r_angle_refined_deg 1.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 21.95 r_dihedral_angle_3_deg 17.166 r_scangle_it 10.862 r_scbond_it 9.301 r_mcangle_it 8.085 r_mcbond_it 7.35 r_dihedral_angle_1_deg 3.453 r_mcbond_other 1.962 r_angle_refined_deg 1.308 r_angle_other_deg 0.895 r_xyhbond_nbd_other 0.254 r_nbd_refined 0.246 r_symmetry_vdw_other 0.218 r_nbtor_refined 0.21 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.122 r_chiral_restr 0.104 r_nbtor_other 0.096 r_symmetry_hbond_refined 0.092 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6920 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection