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Structure of miniSOG reconstituted with riboflavin as a cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Tris-HCl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 15 mM CoCl2
Crystal Properties Matthews coefficient Solvent content 2.04 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.9 α = 90 b = 39.9 β = 90 c = 134.1 γ = 90
Symmetry Space Group P 43 21 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 PIXEL DECTRIS PILATUS 6M-F TOROIDAL MIRROR 2014-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.973 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.07 38.25 100 0.09 0.99 11.5 6.5 91259 12.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.07 1.1 99.9 1.12 0.563 1.12 5.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6GPU 1.07 38.243 48984 2357 99.973 0.131 0.1302 0.1312 0.1553 0.1563 12.796
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] -0.158 -0.158 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.531 r_dihedral_angle_4_deg 19.6 r_dihedral_angle_3_deg 15.169 r_dihedral_angle_1_deg 6.81 r_rigid_bond_restr 5.852 r_lrange_it 3.648 r_lrange_other 3.423 r_scangle_it 3.369 r_scangle_other 3.367 r_scbond_it 2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.531 r_dihedral_angle_4_deg 19.6 r_dihedral_angle_3_deg 15.169 r_dihedral_angle_1_deg 6.81 r_rigid_bond_restr 5.852 r_lrange_it 3.648 r_lrange_other 3.423 r_scangle_it 3.369 r_scangle_other 3.367 r_scbond_it 2.842 r_scbond_other 2.84 r_mcbond_it 2.367 r_mcbond_other 2.334 r_mcangle_it 2.243 r_mcangle_other 2.241 r_angle_refined_deg 2.2 r_angle_other_deg 1.529 r_symmetry_xyhbond_nbd_refined 0.347 r_xyhbond_nbd_refined 0.341 r_nbd_refined 0.289 r_symmetry_nbd_refined 0.263 r_nbd_other 0.233 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.188 r_chiral_restr 0.138 r_symmetry_nbtor_other 0.094 r_metal_ion_refined 0.04 r_bond_refined_d 0.019 r_gen_planes_refined 0.015 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 947 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing