X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2954.4 M sodium formate
Crystal Properties
Matthews coefficientSolvent content
3.1360.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 248.195α = 90
b = 109.738β = 129.41
c = 160.13γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0002ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.366.0799.90.1080.99913.36.7147079
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.341.7850.509

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.345.75139800726699.850.167620.16530.21226RANDOM57.647
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]
-0.650.76-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.275
r_dihedral_angle_2_deg8.055
r_long_range_B_other7.615
r_long_range_B_refined7.612
r_dihedral_angle_1_deg6.435
r_scangle_other5.286
r_mcangle_it3.809
r_mcangle_other3.809
r_scbond_it3.475
r_scbond_other3.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.275
r_dihedral_angle_2_deg8.055
r_long_range_B_other7.615
r_long_range_B_refined7.612
r_dihedral_angle_1_deg6.435
r_scangle_other5.286
r_mcangle_it3.809
r_mcangle_other3.809
r_scbond_it3.475
r_scbond_other3.352
r_mcbond_it2.522
r_mcbond_other2.522
r_angle_refined_deg1.692
r_angle_other_deg0.56
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.001
r_dihedral_angle_4_deg
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 Atoms18919
Nucleic Acid Atoms
Solvent Atoms732
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing