X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental model 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289.150.7M Sodium citrate tribasic dihydrate and 0.1M Bis-Tris propane (pH7.0)
Crystal Properties
Matthews coefficientSolvent content
3.4163.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.763α = 90
b = 106.763β = 90
c = 144.01γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.979SSRFBL17U

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
11.9785.7699.210.1310.1340.027238.724.355651
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)
11.9720.5120.5230.1060.973

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 REPLACEMENTTHROUGHOUT6LNS1.9739.8255651288299.210.137070.135120.17473RANDOM34.366
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]
0.240.24-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.338
r_dihedral_angle_3_deg12.808
r_long_range_B_refined6.852
r_long_range_B_other6.852
r_dihedral_angle_1_deg6.596
r_scangle_other5.276
r_mcangle_it4.783
r_mcangle_other4.783
r_scbond_it4.139
r_scbond_other4.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.338
r_dihedral_angle_3_deg12.808
r_long_range_B_refined6.852
r_long_range_B_other6.852
r_dihedral_angle_1_deg6.596
r_scangle_other5.276
r_mcangle_it4.783
r_mcangle_other4.783
r_scbond_it4.139
r_scbond_other4.138
r_mcbond_it3.842
r_mcbond_other3.835
r_rigid_bond_restr1.496
r_angle_refined_deg0.913
r_angle_other_deg0.34
r_chiral_restr0.05
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3995
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms22

Software

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