X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2890.1M HEPES, pH7.4, 25% PEG10000
Crystal Properties
Matthews coefficientSolvent content
1.831.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.84α = 90
b = 105.88β = 101.16
c = 47.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97917SSRFBL17U1

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
11.3146.549012.26.493345
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.311.34

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 REPLACEMENTTHROUGHOUT5TWD1.4446.5472642379797.610.154260.152580.18725RANDOM18.588
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.473
r_dihedral_angle_4_deg12.644
r_dihedral_angle_3_deg11.926
r_dihedral_angle_1_deg6.857
r_long_range_B_refined5.122
r_long_range_B_other5.066
r_scangle_other4.192
r_scbond_it2.888
r_scbond_other2.887
r_mcangle_other2.413
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.473
r_dihedral_angle_4_deg12.644
r_dihedral_angle_3_deg11.926
r_dihedral_angle_1_deg6.857
r_long_range_B_refined5.122
r_long_range_B_other5.066
r_scangle_other4.192
r_scbond_it2.888
r_scbond_other2.887
r_mcangle_other2.413
r_mcangle_it2.41
r_angle_refined_deg2.38
r_mcbond_it1.74
r_mcbond_other1.733
r_angle_other_deg1.246
r_chiral_restr0.171
r_bond_refined_d0.023
r_gen_planes_refined0.016
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3898
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing