X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5O3K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829523% PEG 4000, 0.05M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0439.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.841α = 90.04
b = 94.85β = 90.29
c = 116.614γ = 91.49
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9793BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.95095.696.83.4235821

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 REPLACEMENTTHROUGHOUT5O3K1.9502358211250195.690.188460.187180.21309RANDOM30.373
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]
0.74-0.61-0.08-0.20.09-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.197
r_sphericity_free28.687
r_dihedral_angle_4_deg16.915
r_rigid_bond_restr15.469
r_dihedral_angle_3_deg15.342
r_sphericity_bonded13.72
r_dihedral_angle_1_deg6.323
r_long_range_B_refined4.98
r_long_range_B_other4.98
r_mcangle_it3.991
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.197
r_sphericity_free28.687
r_dihedral_angle_4_deg16.915
r_rigid_bond_restr15.469
r_dihedral_angle_3_deg15.342
r_sphericity_bonded13.72
r_dihedral_angle_1_deg6.323
r_long_range_B_refined4.98
r_long_range_B_other4.98
r_mcangle_it3.991
r_mcangle_other3.991
r_scangle_other3.722
r_mcbond_other2.923
r_mcbond_it2.922
r_scbond_it2.8
r_scbond_other2.799
r_angle_other_deg1.96
r_angle_refined_deg1.119
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25526
Nucleic Acid Atoms
Solvent Atoms751
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing