X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I3JD_1200011284

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.1291.1514% (w/v) PEG 3350, 0.1 M succinic acid, protein concentration 25 mg/ml
Crystal Properties
Matthews coefficientSolvent content
3.261

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.906α = 90
b = 201.803β = 90
c = 217.869γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.647.9399.60.0740.0860.0440.9989.23.8195423-3.710.9
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)
11.61.6399.80.6350.7380.3730.71.53.9

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 REPLACEMENTTHROUGHOUTD_12000112841.647.93195423958099.550.131890.131220.15402Random selection15.546
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]
0.15-0.09-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.014
r_dihedral_angle_4_deg19.615
r_dihedral_angle_3_deg11.367
r_dihedral_angle_1_deg7.254
r_long_range_B_refined5.357
r_long_range_B_other4.467
r_scangle_other2.835
r_scbond_it1.886
r_scbond_other1.886
r_angle_refined_deg1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.014
r_dihedral_angle_4_deg19.615
r_dihedral_angle_3_deg11.367
r_dihedral_angle_1_deg7.254
r_long_range_B_refined5.357
r_long_range_B_other4.467
r_scangle_other2.835
r_scbond_it1.886
r_scbond_other1.886
r_angle_refined_deg1.67
r_mcangle_it1.555
r_mcangle_other1.555
r_angle_other_deg1.456
r_mcbond_it1.08
r_mcbond_other1.079
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms8468
Nucleic Acid Atoms
Solvent Atoms1670
Heterogen Atoms333

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing