X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7DFM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.42932.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4
Crystal Properties
Matthews coefficientSolvent content
2.141.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.709α = 90
b = 142.709β = 90
c = 72.454γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS EIGER X 16M2019-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1210099.30.16517.98.7110677
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)
122.070.8392.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7DFM247.061110646543499.2390.1680.16510.217630.941
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]
0.8560.4280.856-2.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.067
r_dihedral_angle_3_deg13.709
r_dihedral_angle_4_deg13.47
r_dihedral_angle_1_deg8.316
r_lrange_it5.281
r_lrange_other5.28
r_scangle_it4.161
r_scangle_other4.161
r_mcangle_it2.978
r_mcangle_other2.978
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.067
r_dihedral_angle_3_deg13.709
r_dihedral_angle_4_deg13.47
r_dihedral_angle_1_deg8.316
r_lrange_it5.281
r_lrange_other5.28
r_scangle_it4.161
r_scangle_other4.161
r_mcangle_it2.978
r_mcangle_other2.978
r_scbond_it2.845
r_scbond_other2.844
r_mcbond_it2.256
r_mcbond_other2.256
r_angle_refined_deg1.577
r_angle_other_deg1.365
r_nbd_other0.217
r_metal_ion_refined0.206
r_nbd_refined0.185
r_symmetry_nbd_other0.184
r_nbtor_refined0.18
r_symmetry_nbd_refined0.145
r_xyhbond_nbd_refined0.144
r_symmetry_xyhbond_nbd_refined0.113
r_symmetry_xyhbond_nbd_other0.089
r_symmetry_nbtor_other0.082
r_chiral_restr0.059
r_symmetry_metal_ion_refined0.057
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13486
Nucleic Acid Atoms
Solvent Atoms848
Heterogen Atoms328

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
DENZOdata scaling
MOLREPphasing