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Crystallographic structure of trimeric Riboflavin Synthase from Brucella abortus in complex with 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E0F PDB 4E0F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 292 12% PEG 8000, 10% GLYCEROL, 0.5 M POTASSIUM CHLORIDE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.85 α = 90 b = 92.3 β = 90 c = 99.09 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS 2012-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980110 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 50 99.6 0.075 0.075 15.65 5.81 55235 55235 28.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 98.7 0.773 0.773 1.99 5.75 8736
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 4E0F 1.85 27.09 55210 55210 2765 99.73 0.2016 0.2016 0.1999 0.2339 0.2205 RANDOM 31.4
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] 5.1766 -3.5759 -1.6007
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.12 t_omega_torsion 2.31 t_angle_deg 0.99 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4637 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 126
Software Software Software Name Purpose MxCuBE data collection AMoRE phasing BUSTER refinement XDS data reduction XDS data scaling