X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AEB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4293Crystals were generated from 22 % 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 % 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 13 days in soaking solution containing 15 mM ABH.
Crystal Properties
Matthews coefficientSolvent content
2.244.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.98α = 90
b = 89.98β = 90
c = 69.131γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2Mtransfocator2017-09-06MSINGLE 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
11.6644.9998.90.0980.1260.0770.97162.47320120.47
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)
11.661.6997.50.7360.9460.5870.3852.4

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 REPLACEMENTTHROUGHOUT2AEB1.6644.9969411378598.880.149920.148330.17827RANDOM25.35
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]
4.14.1-8.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_4_deg16.763
r_dihedral_angle_3_deg14.081
r_sphericity_bonded10.765
r_dihedral_angle_1_deg6.158
r_sphericity_free5.487
r_long_range_B_refined4.214
r_long_range_B_other4.09
r_scangle_other2.61
r_mcangle_it2.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_4_deg16.763
r_dihedral_angle_3_deg14.081
r_sphericity_bonded10.765
r_dihedral_angle_1_deg6.158
r_sphericity_free5.487
r_long_range_B_refined4.214
r_long_range_B_other4.09
r_scangle_other2.61
r_mcangle_it2.15
r_mcangle_other2.15
r_scbond_it1.727
r_scbond_other1.725
r_angle_refined_deg1.524
r_mcbond_it1.492
r_mcbond_other1.491
r_angle_other_deg0.826
r_chiral_restr0.083
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4720
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing