4B2K

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CCCPDB ENTRY 2CCC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES (PH 7.5), PEG 400 30% (V/V), 2.5 M NACL, 0.2 M MGCL2
Crystal Properties
Matthews coefficientSolvent content
3.6466

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.301α = 90
b = 142.301β = 90
c = 142.301γ = 90
Symmetry
Space GroupF 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.72099.10.0525.39.3254362
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)
11.71.8950.492.33.4

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 2CCC1.7201332472599.430.1730.171630.19725RANDOM33.471
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_2_deg34.107
r_dihedral_angle_3_deg14.256
r_dihedral_angle_4_deg11.442
r_dihedral_angle_1_deg6.455
r_angle_refined_deg3.299
r_chiral_restr0.292
r_bond_refined_d0.033
r_gen_planes_refined0.017
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.107
r_dihedral_angle_3_deg14.256
r_dihedral_angle_4_deg11.442
r_dihedral_angle_1_deg6.455
r_angle_refined_deg3.299
r_chiral_restr0.292
r_bond_refined_d0.033
r_gen_planes_refined0.017
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms496
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing