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, 100 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0740.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.143α = 90
b = 41.198β = 104.172
c = 72.112γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.8856PAL/PLS5C (4A)

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
11.153094.60.0724.67780785
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)
11.151.170.19511.87

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-VALUE5YUK1.1529.01180768391794.60.1050.10360.127813.117
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]
-0.0010.0010.002-0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.664
r_dihedral_angle_2_deg35.693
r_dihedral_angle_4_deg23.308
r_dihedral_angle_3_deg11.972
r_sphericity_bonded10.536
r_rigid_bond_restr6.91
r_dihedral_angle_1_deg6.899
r_lrange_it4.337
r_lrange_other4.209
r_scangle_it3.949
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.664
r_dihedral_angle_2_deg35.693
r_dihedral_angle_4_deg23.308
r_dihedral_angle_3_deg11.972
r_sphericity_bonded10.536
r_rigid_bond_restr6.91
r_dihedral_angle_1_deg6.899
r_lrange_it4.337
r_lrange_other4.209
r_scangle_it3.949
r_scangle_other3.948
r_scbond_it3.337
r_scbond_other3.337
r_mcangle_other2.715
r_mcangle_it2.608
r_angle_refined_deg2.456
r_mcbond_it2.041
r_mcbond_other1.896
r_angle_other_deg1.878
r_nbd_other0.417
r_symmetry_nbd_refined0.345
r_nbd_refined0.278
r_symmetry_nbd_other0.215
r_symmetry_xyhbond_nbd_refined0.192
r_nbtor_refined0.19
r_chiral_restr0.172
r_xyhbond_nbd_refined0.129
r_symmetry_nbtor_other0.085
r_metal_ion_refined0.071
r_bond_refined_d0.031
r_gen_planes_refined0.014
r_gen_planes_other0.01
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms7

Software

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