6QBR

structure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - mutant S200D, S203D


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J1B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP285PEG 3000 - 6000 15-24 % (w/v) Bicine buffer 0.1 M
Crystal Properties
Matthews coefficientSolvent content
2.2545.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.38α = 90
b = 102.38β = 90
c = 92.336γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.154599.50.0620.0680.99713.35.229991
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.28970.8060.9590.521.13.3

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 REPLACEMENTTHROUGHOUT5j1b2.1544.8128440155099.470.192280.190850.21852RANDOM87.995
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]
0.720.360.72-2.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.145
r_dihedral_angle_3_deg15.278
r_dihedral_angle_4_deg15.051
r_dihedral_angle_1_deg7.098
r_long_range_B_other5.595
r_long_range_B_refined5.594
r_scangle_other3.593
r_mcangle_it3.303
r_mcangle_other3.303
r_scbond_it2.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.145
r_dihedral_angle_3_deg15.278
r_dihedral_angle_4_deg15.051
r_dihedral_angle_1_deg7.098
r_long_range_B_other5.595
r_long_range_B_refined5.594
r_scangle_other3.593
r_mcangle_it3.303
r_mcangle_other3.303
r_scbond_it2.291
r_scbond_other2.29
r_mcbond_other2.096
r_mcbond_it2.095
r_angle_refined_deg1.256
r_angle_other_deg0.928
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3526
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata scaling
PHASERphasing
XDSdata reduction