X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5N6Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529510-13 % PEG 8000 15-20 % ethylene glycol 0.03 M MgCl2 0.1 mM ZnCl2 5 mM Na2S2O4 0.1 M HEPES/NaOH
Crystal Properties
Matthews coefficientSolvent content
2.4850.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.61α = 84.05
b = 79.75β = 72.44
c = 107.16γ = 75.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

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
11.2102.1299.60.1150.0720.99810.16.568322222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2399.10.9010.6860.3384.3

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 REPLACEMENTTHROUGHOUT5N6Y1.2102.126832223569399.610.118270.116890.14458RANDOM15.731
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]
0.140.070.250.29-0.15-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.503
r_sphericity_free22.921
r_dihedral_angle_4_deg18.723
r_rigid_bond_restr13.51
r_dihedral_angle_3_deg12.555
r_sphericity_bonded8.954
r_dihedral_angle_1_deg6.257
r_scbond_other3.958
r_scbond_it3.957
r_long_range_B_refined3.824
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.503
r_sphericity_free22.921
r_dihedral_angle_4_deg18.723
r_rigid_bond_restr13.51
r_dihedral_angle_3_deg12.555
r_sphericity_bonded8.954
r_dihedral_angle_1_deg6.257
r_scbond_other3.958
r_scbond_it3.957
r_long_range_B_refined3.824
r_scangle_other3.722
r_long_range_B_other3.514
r_angle_refined_deg3.339
r_mcbond_it2.363
r_mcbond_other2.363
r_mcangle_it2.22
r_mcangle_other2.219
r_angle_other_deg1.555
r_chiral_restr0.479
r_bond_refined_d0.032
r_gen_planes_refined0.014
r_gen_planes_other0.004
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16520
Nucleic Acid Atoms
Solvent Atoms2652
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing