X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8VR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82932.2-2.5 M ammonium sulfate, 2% hexyleneglycol, 100 mM HEPPS (pH 8)
Crystal Properties
Matthews coefficientSolvent content
2.5251.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.67α = 90
b = 106.67β = 90
c = 180.4γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9792APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.755098.50.06631.58114484
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7895.70.441.94.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.7546.19108704577998.370.188930.186830.2297RANDOM31.142
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.602
r_dihedral_angle_2_deg8.843
r_long_range_B_refined8.042
r_long_range_B_other8.042
r_dihedral_angle_1_deg6.622
r_scangle_other6.515
r_scbond_it4.393
r_scbond_other4.392
r_mcangle_it3.394
r_mcangle_other3.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.602
r_dihedral_angle_2_deg8.843
r_long_range_B_refined8.042
r_long_range_B_other8.042
r_dihedral_angle_1_deg6.622
r_scangle_other6.515
r_scbond_it4.393
r_scbond_other4.392
r_mcangle_it3.394
r_mcangle_other3.394
r_mcbond_it2.518
r_mcbond_other2.517
r_angle_refined_deg1.342
r_angle_other_deg0.447
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms8066
Nucleic Acid Atoms
Solvent Atoms414
Heterogen Atoms270

Software

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