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
2.0439.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.933α = 90.08
b = 94.931β = 90.2
c = 116.587γ = 91.65
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 14.10.9687BESSY14.1

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
11.85092.66.812.07283032

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 REPLACEMENTTHROUGHOUT5O3K1.8502690381399792.590.179580.177410.2215RANDOM27.15
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]
0.89-0.45-0.110.2-0.18-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.122
r_dihedral_angle_4_deg15.1
r_dihedral_angle_3_deg14.12
r_dihedral_angle_1_deg7.072
r_long_range_B_refined4.883
r_long_range_B_other4.883
r_scangle_other3.587
r_mcangle_it2.95
r_mcangle_other2.95
r_scbond_it2.495
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.122
r_dihedral_angle_4_deg15.1
r_dihedral_angle_3_deg14.12
r_dihedral_angle_1_deg7.072
r_long_range_B_refined4.883
r_long_range_B_other4.883
r_scangle_other3.587
r_mcangle_it2.95
r_mcangle_other2.95
r_scbond_it2.495
r_scbond_other2.489
r_mcbond_it2.143
r_mcbond_other2.142
r_angle_refined_deg1.769
r_angle_other_deg0.859
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25585
Nucleic Acid Atoms
Solvent Atoms924
Heterogen Atoms314

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing