X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UBQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5285100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.0339.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.45α = 90
b = 69.245β = 90.22
c = 60.055γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.360.0594.10.0968.711.911542-324.94
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)
12.32.3892.90.442

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1UBQ2.360.05228011092261994.10.2010.1980.246RANDOM29.16
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]
-1.470.191.30.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.248
r_dihedral_angle_4_deg20.874
r_dihedral_angle_3_deg15.697
r_long_range_B_refined9.098
r_long_range_B_other9.096
r_scangle_other7.521
r_dihedral_angle_1_deg6.7
r_scbond_it5.495
r_scbond_other5.495
r_mcangle_it4.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.248
r_dihedral_angle_4_deg20.874
r_dihedral_angle_3_deg15.697
r_long_range_B_refined9.098
r_long_range_B_other9.096
r_scangle_other7.521
r_dihedral_angle_1_deg6.7
r_scbond_it5.495
r_scbond_other5.495
r_mcangle_it4.243
r_mcangle_other4.241
r_mcbond_other3.186
r_mcbond_it3.185
r_angle_other_deg2.078
r_angle_refined_deg1.926
r_chiral_restr0.114
r_bond_refined_d0.016
r_bond_other_d0.012
r_gen_planes_refined0.012
r_gen_planes_other0.01
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 Atoms2366
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms16

Software

Software
Software NamePurpose
EDNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling