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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 2CC6 PDB ENTRY 2CC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 2 M NACL, 0.2 M MGCL2, 0.1 M NA, HEPES 30% (W/V) PEG400, pH 7.50
Crystal Properties Matthews coefficient Solvent content 4.04 69.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.41 α = 90 b = 142.41 β = 90 c = 142.41 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 287 CCD ADSC CCD MIRRORS 2003-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 15 99.8 0.1 19.3 4.2 162605 4.6
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 1.84 100 0.65 4.2 14
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 2CC6 1.8 15 11372 571 100 0.186 0.184 0.1876 0.219 0.2177 RANDOM 28.26
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_1_deg 6.431 r_scangle_it 4.714 r_scbond_it 2.923 r_mcangle_it 2.36 r_angle_refined_deg 1.506 r_mcbond_it 1.318 r_nbd_refined 0.243 r_symmetry_hbond_refined 0.233 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.431 r_scangle_it 4.714 r_scbond_it 2.923 r_mcangle_it 2.36 r_angle_refined_deg 1.506 r_mcbond_it 1.318 r_nbd_refined 0.243 r_symmetry_hbond_refined 0.233 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.13 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 77 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CCP4 phasing