X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP112931.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0941.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.522α = 90
b = 41.23β = 104.055
c = 71.873γ = 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
11.23097.50.0850.0920.0340.9923.17.473833
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)
11.21.2294.70.2970.320.1180.9568.47.3

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-VALUE5YUK1.23073791378197.450.1180.11710.139412.257
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]
-0.1220.015-0.0180.117
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.17
r_dihedral_angle_2_deg34.609
r_dihedral_angle_4_deg25.967
r_sphericity_bonded12.668
r_dihedral_angle_3_deg12.664
r_dihedral_angle_1_deg6.66
r_rigid_bond_restr6.481
r_lrange_it5.349
r_lrange_other4.441
r_scangle_it4.091
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.17
r_dihedral_angle_2_deg34.609
r_dihedral_angle_4_deg25.967
r_sphericity_bonded12.668
r_dihedral_angle_3_deg12.664
r_dihedral_angle_1_deg6.66
r_rigid_bond_restr6.481
r_lrange_it5.349
r_lrange_other4.441
r_scangle_it4.091
r_scangle_other4.09
r_scbond_other3.355
r_scbond_it3.354
r_angle_refined_deg2.552
r_mcangle_other2.056
r_mcangle_it2.016
r_mcbond_it1.573
r_mcbond_other1.372
r_angle_other_deg1.272
r_symmetry_nbd_refined0.331
r_nbd_refined0.294
r_nbd_other0.291
r_symmetry_xyhbond_nbd_refined0.216
r_chiral_restr0.205
r_symmetry_nbd_other0.198
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.147
r_metal_ion_refined0.139
r_symmetry_nbtor_other0.088
r_bond_refined_d0.03
r_gen_planes_refined0.015
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 Atoms279
Heterogen Atoms8

Software

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