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
2.141.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.395α = 90
b = 41.365β = 104.014
c = 72.127γ = 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
11.23095.40.0720.0770.0280.99523.17.672523
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)
11.21.2292.10.3770.4050.1480.9397.27.5

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-VALUE5YUK1.23072507371895.3650.1140.11240.13811.027
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]
-0.0380.075-0.1140.102
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.52
r_dihedral_angle_2_deg34.724
r_dihedral_angle_4_deg23.817
r_sphericity_bonded13.173
r_dihedral_angle_3_deg11.356
r_dihedral_angle_1_deg7.188
r_rigid_bond_restr6.22
r_lrange_it5.134
r_lrange_other4.046
r_scangle_other3.544
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.52
r_dihedral_angle_2_deg34.724
r_dihedral_angle_4_deg23.817
r_sphericity_bonded13.173
r_dihedral_angle_3_deg11.356
r_dihedral_angle_1_deg7.188
r_rigid_bond_restr6.22
r_lrange_it5.134
r_lrange_other4.046
r_scangle_other3.544
r_scangle_it3.542
r_scbond_other2.993
r_scbond_it2.989
r_mcangle_other2.639
r_mcangle_it2.63
r_angle_refined_deg2.382
r_mcbond_it2.101
r_mcbond_other1.814
r_angle_other_deg1.208
r_symmetry_nbd_refined0.321
r_nbd_refined0.293
r_nbd_other0.26
r_metal_ion_refined0.215
r_symmetry_xyhbond_nbd_refined0.202
r_symmetry_nbd_other0.198
r_chiral_restr0.192
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.14
r_symmetry_nbtor_other0.086
r_bond_refined_d0.029
r_gen_planes_refined0.015
r_symmetry_xyhbond_nbd_other0.012
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 Atoms347
Heterogen Atoms15

Software

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