2GM7

TenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.62933 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 coefficientSolvent content
2.7455.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.757α = 90
b = 134.926β = 90
c = 144.029γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2001-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.89099.90.09511.612.4277832778376
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.91001000.586

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1UDD2.819.72275222752115282.540.2340.2340.2310.286RANDOM21.666
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.992
r_dihedral_angle_4_deg19.466
r_dihedral_angle_3_deg16.425
r_scangle_it6.121
r_mcangle_it5.073
r_scbond_it4.56
r_mcbond_it3.702
r_dihedral_angle_1_deg3.26
r_angle_refined_deg1.123
r_angle_other_deg0.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.992
r_dihedral_angle_4_deg19.466
r_dihedral_angle_3_deg16.425
r_scangle_it6.121
r_mcangle_it5.073
r_scbond_it4.56
r_mcbond_it3.702
r_dihedral_angle_1_deg3.26
r_angle_refined_deg1.123
r_angle_other_deg0.878
r_mcbond_other0.68
r_symmetry_vdw_refined0.226
r_symmetry_hbond_refined0.226
r_nbd_refined0.218
r_symmetry_vdw_other0.208
r_nbtor_refined0.191
r_nbd_other0.181
r_xyhbond_nbd_refined0.158
r_nbtor_other0.085
r_chiral_restr0.061
r_bond_refined_d0.009
r_xyhbond_nbd_other0.005
r_bond_other_d0.004
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6822
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms67

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction