X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM MOPS (pH 7) 18-18% PEG-3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.726α = 90
b = 56.837β = 90.04
c = 124.797γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.65098.80.0930.0938.44197128
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.796.30.41122.331639

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 REPLACEMENTTHROUGHOUT3frk1.629.97187240987198.620.150320.148330.18768RANDOM13.501
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]
4.65-1.271.72-6.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_4_deg16.11
r_dihedral_angle_3_deg15.259
r_dihedral_angle_1_deg7.38
r_long_range_B_refined4.648
r_long_range_B_other4.642
r_scangle_other3.619
r_scbond_it2.57
r_scbond_other2.57
r_mcangle_it2.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_4_deg16.11
r_dihedral_angle_3_deg15.259
r_dihedral_angle_1_deg7.38
r_long_range_B_refined4.648
r_long_range_B_other4.642
r_scangle_other3.619
r_scbond_it2.57
r_scbond_other2.57
r_mcangle_it2.381
r_mcangle_other2.381
r_mcbond_it1.797
r_mcbond_other1.797
r_angle_refined_deg1.74
r_angle_other_deg0.83
r_chiral_restr0.111
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11705
Nucleic Acid Atoms
Solvent Atoms712
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing