X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HLIEnsemble comprising chains A and B was placed twice in the asymmetric unit

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.12810.1 M Tris pH 7.1, 0.85 M Na3-citrate, 0.1 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.7154.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.136α = 90
b = 115.539β = 90
c = 189.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9724ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.5449.40399.30.1390.9765.23.947056
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.542.630.4620.757

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.5449.40347000237099.0410.2030.20060.2478Random selection20.459
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]
1.1170.559-1.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg18.321
r_dihedral_angle_3_deg13.452
r_dihedral_angle_6_deg12.64
r_dihedral_angle_2_deg10.387
r_dihedral_angle_1_deg5.82
r_lrange_it3.301
r_lrange_other3.252
r_angle_refined_deg1.461
r_mcangle_it1.208
r_mcangle_other1.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg18.321
r_dihedral_angle_3_deg13.452
r_dihedral_angle_6_deg12.64
r_dihedral_angle_2_deg10.387
r_dihedral_angle_1_deg5.82
r_lrange_it3.301
r_lrange_other3.252
r_angle_refined_deg1.461
r_mcangle_it1.208
r_mcangle_other1.208
r_scangle_it1.146
r_scangle_other1.146
r_mcbond_it0.666
r_mcbond_other0.666
r_scbond_it0.648
r_scbond_other0.648
r_angle_other_deg0.512
r_nbd_refined0.209
r_symmetry_nbd_other0.198
r_nbtor_refined0.181
r_nbd_other0.154
r_xyhbond_nbd_refined0.147
r_symmetry_xyhbond_nbd_refined0.119
r_metal_ion_refined0.107
r_symmetry_nbtor_other0.075
r_chiral_restr0.072
r_symmetry_xyhbond_nbd_other0.048
r_symmetry_nbd_refined0.047
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9048
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing