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Crystallographic structure of trimeric riboflavin synthase from Brucella abortus in complex with roseoflavin
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 7.5 292 12% PEG 8000, 10% GLYCEROL, 0.5 M POTASSIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.04 α = 90 b = 92.57 β = 90 c = 102.58 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 2012-05-13 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 1.78 50 96.1 0.026 0.026 21.24 2.96 60197 60197 34.63
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 1.78 1.89 95.3 0.514 0.514 2.1 2.97 9547
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 4E0F 1.78 32.29 60193 60193 3010 96.07 0.2415 0.2415 0.23987 0.238 0.27278 0.2708 RANDOM 34.964
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] 0.05 -0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.572 r_dihedral_angle_3_deg 13.48 r_dihedral_angle_4_deg 11.181 r_dihedral_angle_1_deg 4.567 r_angle_refined_deg 0.945 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4556 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 116
Software Software Software Name Purpose MxCuBE data collection AMoRE phasing REFMAC refinement XDS data reduction XDS data scaling