7QF2

Structure of miniSOG reconstituted with riboflavin as a cofactor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GPU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM Tris-HCl pH 8.0, 20 mM MgCl2, 28% PEG 4000, 15 mM CoCl2
Crystal Properties
Matthews coefficientSolvent content
2.0439.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.9α = 90
b = 39.9β = 90
c = 134.1γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FTOROIDAL MIRROR2014-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.973ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.0738.251000.090.9911.56.59125912.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.071.199.91.120.5631.125.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6GPU1.0738.24348984235799.9730.1310.13020.155312.796
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]
-0.158-0.1580.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.531
r_dihedral_angle_4_deg19.6
r_dihedral_angle_3_deg15.169
r_dihedral_angle_1_deg6.81
r_rigid_bond_restr5.852
r_lrange_it3.648
r_lrange_other3.423
r_scangle_it3.369
r_scangle_other3.367
r_scbond_it2.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.531
r_dihedral_angle_4_deg19.6
r_dihedral_angle_3_deg15.169
r_dihedral_angle_1_deg6.81
r_rigid_bond_restr5.852
r_lrange_it3.648
r_lrange_other3.423
r_scangle_it3.369
r_scangle_other3.367
r_scbond_it2.842
r_scbond_other2.84
r_mcbond_it2.367
r_mcbond_other2.334
r_mcangle_it2.243
r_mcangle_other2.241
r_angle_refined_deg2.2
r_angle_other_deg1.529
r_symmetry_xyhbond_nbd_refined0.347
r_xyhbond_nbd_refined0.341
r_nbd_refined0.289
r_symmetry_nbd_refined0.263
r_nbd_other0.233
r_symmetry_nbd_other0.212
r_nbtor_refined0.188
r_chiral_restr0.138
r_symmetry_nbtor_other0.094
r_metal_ion_refined0.04
r_bond_refined_d0.019
r_gen_planes_refined0.015
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms947
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing