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
3.261.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 249.373α = 90
b = 109.269β = 129.6
c = 160.658γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1ELETTRA11.2C

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
12.380.3399.80.1040.99912.16.5147134
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)
12.32.341.3630.639

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 REPLACEMENTTHROUGHOUT2.380.01139909721399.760.175550.173220.22167RANDOM52.496
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]
-1.22-0.511.550.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.629
r_dihedral_angle_4_deg19.805
r_dihedral_angle_3_deg17.487
r_dihedral_angle_1_deg7.132
r_long_range_B_refined6.354
r_long_range_B_other6.354
r_scangle_other3.878
r_mcangle_it2.983
r_mcangle_other2.983
r_scbond_it2.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.629
r_dihedral_angle_4_deg19.805
r_dihedral_angle_3_deg17.487
r_dihedral_angle_1_deg7.132
r_long_range_B_refined6.354
r_long_range_B_other6.354
r_scangle_other3.878
r_mcangle_it2.983
r_mcangle_other2.983
r_scbond_it2.783
r_scbond_other2.476
r_mcbond_it1.947
r_mcbond_other1.947
r_angle_refined_deg1.897
r_angle_other_deg1.35
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.005
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 Atoms18520
Nucleic Acid Atoms
Solvent Atoms747
Heterogen Atoms732

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing