X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5291100 mM Citrate, 20% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.6854.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.079α = 90
b = 70.669β = 101.13
c = 77.717γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX21.0Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.5339.898.70.0510.0570.0240.99912.55.285118
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)
11.531.5681.70.3140.350.1520.9412.34.9

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 REPLACEMENTTHROUGHOUT5YEE1.5339.77980852426598.660.151820.150410.17876RANDOM22.246
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]
-0.020.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.756
r_dihedral_angle_4_deg16.875
r_sphericity_free15.762
r_dihedral_angle_3_deg11.425
r_dihedral_angle_1_deg5.272
r_sphericity_bonded3.829
r_long_range_B_refined2.208
r_long_range_B_other1.509
r_angle_refined_deg1.298
r_angle_other_deg0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.756
r_dihedral_angle_4_deg16.875
r_sphericity_free15.762
r_dihedral_angle_3_deg11.425
r_dihedral_angle_1_deg5.272
r_sphericity_bonded3.829
r_long_range_B_refined2.208
r_long_range_B_other1.509
r_angle_refined_deg1.298
r_angle_other_deg0.899
r_mcangle_it0.881
r_mcangle_other0.881
r_rigid_bond_restr0.791
r_mcbond_it0.742
r_mcbond_other0.742
r_scangle_other0.741
r_scbond_it0.698
r_scbond_other0.698
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.003
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 Atoms3807
Nucleic Acid Atoms
Solvent Atoms759
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
ADDREFdata reduction
Aimlessdata scaling
PHASERphasing