X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82931.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0941.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.324α = 90
b = 41.315β = 104.034
c = 72.219γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.9793PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.23098.40.0820.0880.0320.99820.17.474665
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2296.40.6560.7060.2590.8323.87.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5YUK1.23074640382698.3350.1150.11380.139213.704
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]
0.161-0.154-0.090.005
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.738
r_dihedral_angle_2_deg35.559
r_dihedral_angle_4_deg23.997
r_sphericity_bonded14.746
r_dihedral_angle_3_deg11.996
r_lrange_it7.848
r_dihedral_angle_1_deg6.975
r_rigid_bond_restr6.076
r_lrange_other4.803
r_scangle_other3.983
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.738
r_dihedral_angle_2_deg35.559
r_dihedral_angle_4_deg23.997
r_sphericity_bonded14.746
r_dihedral_angle_3_deg11.996
r_lrange_it7.848
r_dihedral_angle_1_deg6.975
r_rigid_bond_restr6.076
r_lrange_other4.803
r_scangle_other3.983
r_scangle_it3.982
r_scbond_other3.829
r_scbond_it3.825
r_mcangle_other3.564
r_mcangle_it3.544
r_mcbond_it2.519
r_mcbond_other2.385
r_angle_refined_deg2.284
r_angle_other_deg1.196
r_symmetry_xyhbond_nbd_other0.443
r_symmetry_nbd_refined0.33
r_nbd_refined0.313
r_nbd_other0.263
r_xyhbond_nbd_refined0.245
r_chiral_restr0.194
r_symmetry_nbd_other0.189
r_symmetry_xyhbond_nbd_refined0.189
r_nbtor_refined0.187
r_symmetry_nbtor_other0.086
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing