X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A07 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.7767.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.504α = 90
b = 273.006β = 90
c = 186.279γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.944.8299.890.0660.0720.99915.366.9306207
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9680.7340.7920.81.91

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 REPLACEMENTTHROUGHOUT5A071.944.822910961512099.890.161320.160290.1812RANDOM39.783
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]
1.28-1.860.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_dihedral_angle_4_deg14.493
r_dihedral_angle_3_deg11.922
r_dihedral_angle_1_deg6.218
r_long_range_B_refined5.636
r_long_range_B_other5.306
r_scangle_other3.441
r_mcangle_it2.443
r_mcangle_other2.443
r_scbond_it2.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.168
r_dihedral_angle_4_deg14.493
r_dihedral_angle_3_deg11.922
r_dihedral_angle_1_deg6.218
r_long_range_B_refined5.636
r_long_range_B_other5.306
r_scangle_other3.441
r_mcangle_it2.443
r_mcangle_other2.443
r_scbond_it2.156
r_scbond_other2.156
r_mcbond_it1.632
r_mcbond_other1.632
r_angle_refined_deg1.304
r_angle_other_deg0.906
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 Atoms18408
Nucleic Acid Atoms
Solvent Atoms1980
Heterogen Atoms295

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing