X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529316-21% PEG-3350, 300 mM KCl, 100 mM HEPES, 5 mM neamine, 1 mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.2244.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.363α = 90
b = 107.363β = 98.24
c = 217.528γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9498APS19-BM

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
11.65087.20.0490.04938.43.9367186
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.66700.10.17.92.6

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 REPLACEMENTTHROUGHOUT6cbk1.6303488371834687.330.198560.196220.24283RANDOM23.734
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]
-1.68-0.063.07-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.218
r_dihedral_angle_4_deg17.668
r_dihedral_angle_3_deg15.102
r_dihedral_angle_1_deg6.535
r_long_range_B_refined5.685
r_long_range_B_other5.587
r_scangle_other4.71
r_scbond_it3.415
r_scbond_other3.414
r_mcangle_it3.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.218
r_dihedral_angle_4_deg17.668
r_dihedral_angle_3_deg15.102
r_dihedral_angle_1_deg6.535
r_long_range_B_refined5.685
r_long_range_B_other5.587
r_scangle_other4.71
r_scbond_it3.415
r_scbond_other3.414
r_mcangle_it3.212
r_mcangle_other3.212
r_mcbond_it2.588
r_mcbond_other2.588
r_angle_refined_deg1.833
r_angle_other_deg0.938
r_chiral_restr0.12
r_bond_refined_d0.011
r_gen_planes_refined0.007
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 Atoms24768
Nucleic Acid Atoms
Solvent Atoms2470
Heterogen Atoms297

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing