X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2890.1 M HEPES, pH7.4, 25% PEG10000
Crystal Properties
Matthews coefficientSolvent content
1.8132.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.16α = 90
b = 105.54β = 101.09
c = 47.59γ = 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
11.1946.774.818.66103975
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.191.221.83.1

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 REPLACEMENTTHROUGHOUT5TWD1.4440.8673647381698.210.149160.147710.17778RANDOM14.832
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]
0.040.55-0.310.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.446
r_dihedral_angle_3_deg11.883
r_dihedral_angle_4_deg10.013
r_dihedral_angle_1_deg6.784
r_long_range_B_refined4.593
r_long_range_B_other4.415
r_scangle_other3.442
r_scbond_it2.327
r_scbond_other2.327
r_mcangle_it2.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.446
r_dihedral_angle_3_deg11.883
r_dihedral_angle_4_deg10.013
r_dihedral_angle_1_deg6.784
r_long_range_B_refined4.593
r_long_range_B_other4.415
r_scangle_other3.442
r_scbond_it2.327
r_scbond_other2.327
r_mcangle_it2.083
r_mcangle_other2.074
r_angle_refined_deg1.898
r_angle_other_deg1.61
r_mcbond_it1.397
r_mcbond_other1.379
r_chiral_restr0.205
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
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 Atoms3898
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing