X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E6U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP282.150.70-0.75 M succinic acid pH 7.0, 0.1 M bis-tris-propane pH 7.0.
Crystal Properties
Matthews coefficientSolvent content
2.6353.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.587α = 90
b = 120.257β = 90
c = 143.019γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12723APS21-ID-D

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
11.78692.04399.30.0990.1050.0340.99913.59.590992
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)
11.7861.79293.71.0831.1580.3930.8792.18.2

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 REPLACEMENTTHROUGHOUT3E6U1.792585974446999.240.182470.181450.20186RANDOM29.95
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]
-2.264.7-2.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.372
r_dihedral_angle_4_deg20.794
r_dihedral_angle_3_deg15.253
r_dihedral_angle_1_deg6.389
r_long_range_B_refined5.321
r_scbond_it2.631
r_mcangle_it2.298
r_mcbond_it1.564
r_angle_refined_deg1.215
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.372
r_dihedral_angle_4_deg20.794
r_dihedral_angle_3_deg15.253
r_dihedral_angle_1_deg6.389
r_long_range_B_refined5.321
r_scbond_it2.631
r_mcangle_it2.298
r_mcbond_it1.564
r_angle_refined_deg1.215
r_chiral_restr0.098
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6404
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
Aimlessdata scaling
PHASERphasing