X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52960.1 M Tris-HCl, PEG 10,000 (20% w/v)
Crystal Properties
Matthews coefficientSolvent content
2.1141.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.23α = 90
b = 60.41β = 90
c = 264.1γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.00001ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.542.2995.30.1830.0840.97565.96972610.36
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)
11.51.5295.30.1180.1320.0580.9757.9

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 REPLACEMENTTHROUGHOUT1YLT1.542.2965806345090.710.191010.18940.22212RANDOM13.21
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]
0.32-0.06-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_3_deg12.637
r_dihedral_angle_4_deg10.305
r_dihedral_angle_1_deg6.527
r_long_range_B_refined5.558
r_angle_refined_deg2.122
r_scbond_it2.078
r_mcangle_it1.544
r_mcbond_it1.064
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_3_deg12.637
r_dihedral_angle_4_deg10.305
r_dihedral_angle_1_deg6.527
r_long_range_B_refined5.558
r_angle_refined_deg2.122
r_scbond_it2.078
r_mcangle_it1.544
r_mcbond_it1.064
r_chiral_restr0.123
r_bond_refined_d0.035
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3897
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms28

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing