X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XK9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.66 M sodium citrate pH 7.5, 0.54 mM sodium azide, 0.3 mM dithiothreitol, 0.5 mM PJ34 1.1 M sodium citrate pH 7.5, 0.9 mM sodium azide, 0.5 mM dithiothreitol 0.5 mM PJ34
Crystal Properties
Matthews coefficientSolvent content
2.0138.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.373α = 90
b = 48.188β = 90
c = 99.002γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.03320CLSI08ID-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
11.4749.599.40.0670.99916.518.2432473
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)
11.471.5496.90.9590.8052.147.76

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 REPLACEMENTTHROUGHOUT1XK91.4749.530481154999.940.17810.177420.19195RANDOM28.335
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]
0.26-1.311.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.416
r_dihedral_angle_4_deg16.998
r_dihedral_angle_3_deg11.816
r_long_range_B_other8.863
r_long_range_B_refined8.844
r_scangle_other6.735
r_dihedral_angle_1_deg5.683
r_mcangle_it4.779
r_mcangle_other4.775
r_scbond_it4.482
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.416
r_dihedral_angle_4_deg16.998
r_dihedral_angle_3_deg11.816
r_long_range_B_other8.863
r_long_range_B_refined8.844
r_scangle_other6.735
r_dihedral_angle_1_deg5.683
r_mcangle_it4.779
r_mcangle_other4.775
r_scbond_it4.482
r_scbond_other4.48
r_mcbond_it3.17
r_mcbond_other3.132
r_angle_refined_deg2.439
r_angle_other_deg1.273
r_chiral_restr0.173
r_bond_refined_d0.027
r_gen_planes_refined0.015
r_gen_planes_other0.005
r_bond_other_d0.002
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 Atoms1608
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing