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Structure of the tirandamycin-bound FAD-dependent tirandamycin oxidase TamL in P21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y08 PDB ENTRY 2Y08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 296 9% PEG 4000, 0.2 M MGCL, 23 DEGREES CELSIUS., pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.088 α = 90 b = 106.171 β = 94.63 c = 151.172 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 110 CCD ADSC QUANTUM 315r MIRRORS 2010-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.79 19.82 76.7 0.06 10.6 2.9 161395 1.5 18.8
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 1.79 1.89 26.9 0.24 2.4 1.9
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 (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 2Y08 1.79 150.68 152628 8138 76.45 0.14969 0.14603 0.1456 0.219 0.2177 RANDOM 18.683
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] 0.14 -0.17 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.344 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 14.884 r_dihedral_angle_1_deg 6.203 r_scangle_it 6.057 r_scbond_it 4.099 r_mcangle_it 2.545 r_rigid_bond_restr 2.433 r_angle_refined_deg 2.02 r_mcbond_it 1.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.344 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 14.884 r_dihedral_angle_1_deg 6.203 r_scangle_it 6.057 r_scbond_it 4.099 r_mcangle_it 2.545 r_rigid_bond_restr 2.433 r_angle_refined_deg 2.02 r_mcbond_it 1.644 r_chiral_restr 0.14 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 Atoms Number Protein Atoms 14985 Nucleic Acid Atoms Solvent Atoms 2000 Heterogen Atoms 380
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing