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
2.141.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.419α = 90
b = 41.398β = 104.04
c = 72.191γ = 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
11.23096.10.0470.0510.0190.99840.67.573282
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)
11.21.22930.2270.2440.090.97510.17.3

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-VALUE5YUK1.23073217374896.090.1130.11210.136411.329
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]
-0.121-0.0240.0190.101
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free50.339
r_dihedral_angle_2_deg34.886
r_dihedral_angle_4_deg23.356
r_sphericity_bonded12.299
r_dihedral_angle_3_deg11.544
r_dihedral_angle_1_deg7.032
r_rigid_bond_restr6.084
r_lrange_it4.717
r_lrange_other3.981
r_scangle_other3.854
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free50.339
r_dihedral_angle_2_deg34.886
r_dihedral_angle_4_deg23.356
r_sphericity_bonded12.299
r_dihedral_angle_3_deg11.544
r_dihedral_angle_1_deg7.032
r_rigid_bond_restr6.084
r_lrange_it4.717
r_lrange_other3.981
r_scangle_other3.854
r_scangle_it3.852
r_mcangle_other3.546
r_mcangle_it3.521
r_mcbond_it3.064
r_scbond_other2.869
r_scbond_it2.866
r_angle_refined_deg2.352
r_mcbond_other2.033
r_angle_other_deg1.247
r_symmetry_nbd_refined0.308
r_nbd_other0.3
r_nbd_refined0.29
r_symmetry_xyhbond_nbd_refined0.231
r_symmetry_nbd_other0.203
r_chiral_restr0.194
r_nbtor_refined0.185
r_metal_ion_refined0.177
r_xyhbond_nbd_refined0.138
r_symmetry_nbtor_other0.084
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_gen_planes_other0.004
r_bond_other_d0.003
r_symmetry_xyhbond_nbd_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms15

Software

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