X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YLT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1 M Sodium HEPES pH7.5, 25% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.0439.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.418α = 90
b = 41.418β = 90
c = 230.493γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2020-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.11ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.6735.497.310.07199.12717112.98
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6711.730.18

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 REPLACEMENTTHROUGHOUT1YLT1.6735.425763140697.30.173830.170550.23292RANDOM20.156
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]
-0.04-0.02-0.040.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.273
r_sphericity_bonded24.489
r_dihedral_angle_3_deg14.911
r_dihedral_angle_4_deg14.736
r_dihedral_angle_1_deg6.764
r_rigid_bond_restr5.62
r_long_range_B_other5.505
r_long_range_B_refined5.504
r_scangle_other4.793
r_scbond_it4.363
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.273
r_sphericity_bonded24.489
r_dihedral_angle_3_deg14.911
r_dihedral_angle_4_deg14.736
r_dihedral_angle_1_deg6.764
r_rigid_bond_restr5.62
r_long_range_B_other5.505
r_long_range_B_refined5.504
r_scangle_other4.793
r_scbond_it4.363
r_scbond_other4.361
r_mcangle_it3.983
r_mcangle_other3.981
r_mcbond_it3.535
r_mcbond_other3.529
r_angle_refined_deg2.171
r_angle_other_deg1.205
r_chiral_restr0.141
r_bond_refined_d0.026
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
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
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1952
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms8

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement