X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MF6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.72931.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Crystal Properties
Matthews coefficientSolvent content
2.6353.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.413α = 90
b = 91.413β = 90
c = 144.158γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.945.7199.90.10.99913.26.9536351.241.14
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.92.0199.31.630.3781.26.6

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 REPLACEMENTTHROUGHOUT5MF61.943.5751587204799.870.152930.151640.18692RANDOM44.115
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]
-17.13-17.1334.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.354
r_dihedral_angle_4_deg19.509
r_dihedral_angle_3_deg15.425
r_long_range_B_refined10.103
r_long_range_B_other10.102
r_scangle_other8.14
r_dihedral_angle_1_deg7.018
r_scbond_it5.869
r_scbond_other5.868
r_mcangle_it5.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.354
r_dihedral_angle_4_deg19.509
r_dihedral_angle_3_deg15.425
r_long_range_B_refined10.103
r_long_range_B_other10.102
r_scangle_other8.14
r_dihedral_angle_1_deg7.018
r_scbond_it5.869
r_scbond_other5.868
r_mcangle_it5.437
r_mcangle_other5.437
r_mcbond_it4.47
r_mcbond_other4.469
r_angle_other_deg2.389
r_angle_refined_deg2.106
r_chiral_restr0.1
r_bond_other_d0.034
r_gen_planes_other0.024
r_bond_refined_d0.014
r_gen_planes_refined0.014
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4360
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms201

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing