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Complexes of Dodecin with Flavin and Flavin-like Ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CC9 PDB ENTRY 2CC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M MGCL2, 2.0 M NACL, 0.1 M NA HEPES PH 7.5 AND 30% PEG400
Crystal Properties Matthews coefficient Solvent content 3.51 64.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.39 α = 90 b = 142.39 β = 90 c = 142.39 γ = 90
Symmetry Space Group F 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC CCD MIRRORS 2005-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.8 20 99.7 0.11 14.58 10.27 122830 3.5
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 1.8 1.91 99.6 0.58 3.54 10.29
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 2CC9 1.8 20 11369 571 99.9 0.188 0.187 0.1883 0.209 0.2127 RANDOM 25.08
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.324 r_dihedral_angle_3_deg 16.461 r_dihedral_angle_4_deg 8.849 r_dihedral_angle_1_deg 5.997 r_scangle_it 5.255 r_scbond_it 3.199 r_mcangle_it 2.317 r_angle_refined_deg 2.146 r_mcbond_it 1.264 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.324 r_dihedral_angle_3_deg 16.461 r_dihedral_angle_4_deg 8.849 r_dihedral_angle_1_deg 5.997 r_scangle_it 5.255 r_scbond_it 3.199 r_mcangle_it 2.317 r_angle_refined_deg 2.146 r_mcbond_it 1.264 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.223 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.135 r_symmetry_metal_ion_refined 0.094 r_metal_ion_refined 0.072 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 495 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling