X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JKG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M MES pH 6.5, 1.6 M magnesium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.54α = 90
b = 74.09β = 90
c = 155.81γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9792APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.877.999.90.1020.99511.65.419083
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9599.90.4120.9045.3

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 REPLACEMENTTHROUGHOUT1JKG2.866.9117130190499.870.217050.212070.26259RANDOM40.085
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]
4.45-2.68-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.267
r_dihedral_angle_4_deg23.525
r_dihedral_angle_3_deg20.566
r_long_range_B_refined7.426
r_long_range_B_other7.425
r_dihedral_angle_1_deg7.386
r_scangle_other4.952
r_mcangle_it4.63
r_mcangle_other4.629
r_scbond_other3.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.267
r_dihedral_angle_4_deg23.525
r_dihedral_angle_3_deg20.566
r_long_range_B_refined7.426
r_long_range_B_other7.425
r_dihedral_angle_1_deg7.386
r_scangle_other4.952
r_mcangle_it4.63
r_mcangle_other4.629
r_scbond_other3.053
r_scbond_it3.052
r_mcbond_it2.862
r_mcbond_other2.862
r_angle_refined_deg1.565
r_angle_other_deg1.285
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms5101
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing