X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U8Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28150mM HEPES pH 6.5, 39% sodium polyacrylate
Crystal Properties
Matthews coefficientSolvent content
2.7655.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.695α = 90
b = 100.695β = 90
c = 448.38γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

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
12.250980.07910.433.4133339
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)
12.22.396.11.08920826

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5U8Y2.249.12127272606798.040.180020.178780.20529RANDOM52.503
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]
0.740.370.74-2.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.081
r_dihedral_angle_4_deg14.232
r_dihedral_angle_3_deg13.29
r_long_range_B_refined7.375
r_long_range_B_other7.353
r_dihedral_angle_1_deg6.692
r_scangle_other4.962
r_mcangle_it4.026
r_mcangle_other4.026
r_scbond_it3.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.081
r_dihedral_angle_4_deg14.232
r_dihedral_angle_3_deg13.29
r_long_range_B_refined7.375
r_long_range_B_other7.353
r_dihedral_angle_1_deg6.692
r_scangle_other4.962
r_mcangle_it4.026
r_mcangle_other4.026
r_scbond_it3.144
r_scbond_other3.144
r_mcbond_it2.713
r_mcbond_other2.713
r_angle_refined_deg1.359
r_angle_other_deg0.916
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms15924
Nucleic Acid Atoms
Solvent Atoms955
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing