X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q9P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4293Crystals were generated from 22.5 % PEG 1500, 0.2 M MIB buffer pH 4.0 (sodium malonate, imidazole and boric acid in a 2:3:3 molar ratio). Crystals were equilibrated to soaking solution (22.5 % PEG 1500, 0.2 M MMT buffer pH 9.0 (DL-malic acid, MES, Tris base in a 1:2:2 molar ratio). Subsequently, crystals were gradually soaked for 4 days in soaking solution containing 15 mM compound 3.
Crystal Properties
Matthews coefficientSolvent content
2.244.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.13α = 90
b = 90.13β = 90
c = 69.111γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2Mtransfocator2017-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

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
11.6151.7496.90.0580.0760.0490.9966.927909020.01
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)
11.611.64960.6580.8680.5610.3682.1

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 REPLACEMENTTHROUGHOUT6Q9P1.6151.7474978410596.850.1490.147440.177RANDOM24.684
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]
3.483.48-6.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.348
r_dihedral_angle_4_deg14.635
r_dihedral_angle_3_deg12.91
r_dihedral_angle_1_deg6.164
r_sphericity_bonded5.325
r_sphericity_free4.94
r_long_range_B_refined3.683
r_long_range_B_other3.657
r_scangle_other1.999
r_mcangle_it1.991
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.348
r_dihedral_angle_4_deg14.635
r_dihedral_angle_3_deg12.91
r_dihedral_angle_1_deg6.164
r_sphericity_bonded5.325
r_sphericity_free4.94
r_long_range_B_refined3.683
r_long_range_B_other3.657
r_scangle_other1.999
r_mcangle_it1.991
r_mcangle_other1.991
r_angle_refined_deg1.356
r_mcbond_it1.277
r_mcbond_other1.277
r_scbond_it1.274
r_scbond_other1.266
r_angle_other_deg0.806
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4830
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing