X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WN8PDB entry 5WN8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH10277100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 200 mM sodium chloride, 20% w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
3.0159.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.604α = 90
b = 96.565β = 90
c = 130.764γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2018-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.9429.3699.90.1230.0499.27.423694
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.943.11002.0430.7950.331.17.5

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 REPLACEMENTTHROUGHOUTPDB entry 5WN82.9429.3622499114599.790.193010.190690.2399RANDOM109.659
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]
-3.030.532.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.746
r_dihedral_angle_3_deg19.858
r_dihedral_angle_4_deg16.62
r_long_range_B_refined11.934
r_long_range_B_other11.933
r_mcangle_it8.466
r_mcangle_other8.464
r_dihedral_angle_1_deg8.206
r_scangle_other7.78
r_mcbond_it5.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.746
r_dihedral_angle_3_deg19.858
r_dihedral_angle_4_deg16.62
r_long_range_B_refined11.934
r_long_range_B_other11.933
r_mcangle_it8.466
r_mcangle_other8.464
r_dihedral_angle_1_deg8.206
r_scangle_other7.78
r_mcbond_it5.347
r_mcbond_other5.347
r_scbond_it4.65
r_scbond_other4.649
r_angle_other_deg0.694
r_angle_refined_deg0.515
r_chiral_restr0.026
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_refined_d0.002
r_bond_other_d0.001
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 Atoms5846
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing