2CCC

Complexes of Dodecin with Flavin and Flavin-like Ligands


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CC6PDB ENTRY 2CC6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52 M NACL, 0.2 M MGCL2, 0.1 M NA, HEPES 30% (W/V), PEG400, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
4.0869.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.85α = 90
b = 142.85β = 90
c = 142.85γ = 90
Symmetry
Space GroupF 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDADSC CCDMIRRORS2004-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.72099.70.0820.710.2228643.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.81000.653.810.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2CC61.7201354970799.90.1850.1840.202RANDOM22.77
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.01
r_scangle_it4.51
r_scbond_it2.731
r_mcangle_it2.106
r_angle_refined_deg1.402
r_mcbond_it1.145
r_nbd_refined0.219
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.145
r_symmetry_vdw_refined0.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.01
r_scangle_it4.51
r_scbond_it2.731
r_mcangle_it2.106
r_angle_refined_deg1.402
r_mcbond_it1.145
r_nbd_refined0.219
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.145
r_symmetry_vdw_refined0.137
r_chiral_restr0.118
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms495
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing