2Y3S

Structure of the tirandamycine-bound FAD-dependent tirandamycin oxidase TamL in C2 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y08PDB ENTRY 2Y08

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52969% PEG 4000, 0.2M MGSO4, 23 DEGREES C., pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5952.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.046α = 90
b = 105.786β = 110.67
c = 70.971γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315rMIRRORS2010-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.6786.7692.90.116.23.81201841.5
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)
11.671.7664.20.511.42.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Y081.6786.76114137602692.80.163580.16060.22039RANDOM18.15
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]
1.120.861.59-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.97
r_dihedral_angle_4_deg19.061
r_dihedral_angle_3_deg14.768
r_scangle_it6.782
r_dihedral_angle_1_deg6.369
r_scbond_it4.881
r_mcangle_it3.076
r_rigid_bond_restr2.606
r_mcbond_it2.101
r_angle_refined_deg2.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.97
r_dihedral_angle_4_deg19.061
r_dihedral_angle_3_deg14.768
r_scangle_it6.782
r_dihedral_angle_1_deg6.369
r_scbond_it4.881
r_mcangle_it3.076
r_rigid_bond_restr2.606
r_mcbond_it2.101
r_angle_refined_deg2.096
r_chiral_restr0.153
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7599
Nucleic Acid Atoms
Solvent Atoms888
Heterogen Atoms201

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing