X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y4J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293PEG 20000 16-26%, MES 0.1M pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.7154.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.096α = 90
b = 129.493β = 90
c = 86.78γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.764.7598.7112.612.755830
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.730.752.2

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 REPLACEMENTTHROUGHOUT6Y4J1.764.7553043272998.460.168960.167690.19353RANDOM20.158
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.405
r_dihedral_angle_4_deg16.542
r_dihedral_angle_3_deg13.15
r_dihedral_angle_1_deg7.065
r_long_range_B_refined6.385
r_long_range_B_other6.239
r_scangle_other4.802
r_scbond_it3.183
r_scbond_other3.169
r_mcangle_other2.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.405
r_dihedral_angle_4_deg16.542
r_dihedral_angle_3_deg13.15
r_dihedral_angle_1_deg7.065
r_long_range_B_refined6.385
r_long_range_B_other6.239
r_scangle_other4.802
r_scbond_it3.183
r_scbond_other3.169
r_mcangle_other2.784
r_mcangle_it2.771
r_mcbond_it1.931
r_mcbond_other1.877
r_angle_refined_deg1.723
r_angle_other_deg1.448
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3322
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing