X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82951.0 M sodium citrate, 0.1 M Imidazole pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.0740.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.519α = 90
b = 255.388β = 90
c = 36.179γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002018-01-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.572599.80.060.0630.0179.612.7114161
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)
11.571.6499.80.5130.5370.1580.95511.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5YVK1.5824.68108404568599.60.127630.124850.18032RANDOM24.36
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]
-1.411.88-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.093
r_sphericity_free29.439
r_sphericity_bonded23.915
r_dihedral_angle_4_deg23.742
r_dihedral_angle_3_deg14.721
r_dihedral_angle_1_deg6.961
r_scangle_other6.81
r_long_range_B_refined6.493
r_long_range_B_other6.364
r_scbond_it6.191
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.093
r_sphericity_free29.439
r_sphericity_bonded23.915
r_dihedral_angle_4_deg23.742
r_dihedral_angle_3_deg14.721
r_dihedral_angle_1_deg6.961
r_scangle_other6.81
r_long_range_B_refined6.493
r_long_range_B_other6.364
r_scbond_it6.191
r_scbond_other6.188
r_rigid_bond_restr5.888
r_mcangle_it4.057
r_mcangle_other4.056
r_mcbond_it3.533
r_mcbond_other3.525
r_angle_refined_deg1.48
r_angle_other_deg1.052
r_chiral_restr0.082
r_gen_planes_refined0.011
r_bond_refined_d0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6120
Nucleic Acid Atoms
Solvent Atoms816
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing