X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WKN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5295100 mM Bis-Tris pH 5.5, 200 mM Magnesium Chloride, 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.140.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.367α = 87.54
b = 75.288β = 89.05
c = 90.437γ = 71.13
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252017-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.790.3597.30.998.14.2179940
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7395.70.842.14.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4WKN1.790.35171111879797.330.231190.230330.24786RANDOM23.148
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]
-0.32-0.640.060.190.07-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.144
r_dihedral_angle_4_deg23.054
r_dihedral_angle_3_deg13.647
r_dihedral_angle_1_deg6.253
r_long_range_B_refined4.375
r_long_range_B_other4.375
r_scangle_other2.103
r_mcangle_it1.796
r_mcangle_other1.796
r_angle_refined_deg1.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.144
r_dihedral_angle_4_deg23.054
r_dihedral_angle_3_deg13.647
r_dihedral_angle_1_deg6.253
r_long_range_B_refined4.375
r_long_range_B_other4.375
r_scangle_other2.103
r_mcangle_it1.796
r_mcangle_other1.796
r_angle_refined_deg1.334
r_scbond_it1.256
r_scbond_other1.256
r_mcbond_it1.034
r_mcbond_other1.034
r_angle_other_deg0.894
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms14049
Nucleic Acid Atoms
Solvent Atoms1710
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing