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
2.141.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.39α = 90
b = 41.466β = 104.106
c = 72.147γ = 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
11.23094.60.0560.0610.0220.99929.97.672147
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)
11.21.2291.90.2030.2180.0790.98111.87.5

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-VALUE5YUK1.23072112369694.6380.1050.10330.127312.078
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]
-0.0980.052-0.0060.069
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free45.232
r_dihedral_angle_2_deg34.415
r_dihedral_angle_4_deg23.373
r_sphericity_bonded11.92
r_dihedral_angle_3_deg11.808
r_dihedral_angle_1_deg7.048
r_rigid_bond_restr6.408
r_lrange_it5.557
r_lrange_other4.509
r_mcangle_other3.943
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free45.232
r_dihedral_angle_2_deg34.415
r_dihedral_angle_4_deg23.373
r_sphericity_bonded11.92
r_dihedral_angle_3_deg11.808
r_dihedral_angle_1_deg7.048
r_rigid_bond_restr6.408
r_lrange_it5.557
r_lrange_other4.509
r_mcangle_other3.943
r_mcangle_it3.934
r_scangle_it3.253
r_scangle_other3.252
r_mcbond_it3.171
r_mcbond_other3.109
r_scbond_it2.858
r_scbond_other2.858
r_angle_refined_deg2.368
r_angle_other_deg1.23
r_nbd_refined0.312
r_symmetry_nbd_refined0.305
r_nbd_other0.279
r_chiral_restr0.199
r_symmetry_nbd_other0.19
r_nbtor_refined0.185
r_symmetry_xyhbond_nbd_refined0.165
r_xyhbond_nbd_refined0.148
r_symmetry_xyhbond_nbd_other0.146
r_symmetry_nbtor_other0.085
r_metal_ion_refined0.066
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms13

Software

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