X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5291PEG 3350, sodium citrate, bis-tris propane
Crystal Properties
Matthews coefficientSolvent content
3.2462

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.004α = 90
b = 112.004β = 90
c = 304.82γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
13.05971000.1510.0520.99710.79.943285
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.053.171001.6070.5610.59210

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 REPLACEMENTTHROUGHOUT1KYZ3.059741153206799.960.212470.210310.25569RANDOM57.14
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]
-1.44-0.72-1.444.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.757
r_dihedral_angle_3_deg20.399
r_dihedral_angle_4_deg18.904
r_long_range_B_refined11.855
r_long_range_B_other11.855
r_mcangle_it8.731
r_mcangle_other8.73
r_scangle_other8.512
r_dihedral_angle_1_deg7.822
r_mcbond_it5.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.757
r_dihedral_angle_3_deg20.399
r_dihedral_angle_4_deg18.904
r_long_range_B_refined11.855
r_long_range_B_other11.855
r_mcangle_it8.731
r_mcangle_other8.73
r_scangle_other8.512
r_dihedral_angle_1_deg7.822
r_mcbond_it5.726
r_mcbond_other5.726
r_scbond_it5.172
r_scbond_other5.172
r_angle_refined_deg1.597
r_angle_other_deg1.289
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms10068
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing