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Crystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes with FMN bound at 2.05 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 3 mM TtnD1, 3 mM MnCl2, 0.5 mM FMN, 20% (v/v) glycerol in precipitant solution
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.07 α = 90 b = 116.109 β = 90 c = 193.969 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 CCD RAYONIX MX-225 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.05 48.5 97.8 0.134 0.144 0.053 0.998 10.7 7.24 37316 40.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 96.4 1.392 1.392 1.522 0.604 0.577 0.6 6 2624
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 FOURIER SYNTHESIS THROUGHOUT 6DA7 2.05 19.98 37267 1437 99.7 0.194 0.193 0.1965 0.216 0.2234 RANDOM 54.85
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] 2.4327 -7.7616 5.3289
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.13 t_omega_torsion 3.71 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.13 t_omega_torsion 3.71 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3553 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 107
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX phasing BUSTER refinement PDB_EXTRACT data extraction