X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KD71KD7 , 7FAB
experimental modelPDB 7FAB1KD7 , 7FAB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2939% (w/v) PEG4000, 0.1 M MgCl2, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.2662.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.687α = 90
b = 135.499β = 91.88
c = 138.18γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.9138.1198.711.243.36109365
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.1595.43.05

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 REPLACEMENTTHROUGHOUT1KD7 , 7FAB2.9138.1110871165499.010.191060.190820.23128RANDOM59.251
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]
0.89-1.560.29-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.688
r_dihedral_angle_4_deg16.333
r_dihedral_angle_3_deg13.846
r_dihedral_angle_1_deg7.616
r_long_range_B_refined6.105
r_long_range_B_other6.104
r_scangle_other4.689
r_mcangle_it3.571
r_mcangle_other3.571
r_scbond_it3.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.688
r_dihedral_angle_4_deg16.333
r_dihedral_angle_3_deg13.846
r_dihedral_angle_1_deg7.616
r_long_range_B_refined6.105
r_long_range_B_other6.104
r_scangle_other4.689
r_mcangle_it3.571
r_mcangle_other3.571
r_scbond_it3.125
r_scbond_other3.125
r_mcbond_it2.222
r_mcbond_other2.222
r_angle_refined_deg1.524
r_angle_other_deg1.197
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25879
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing