X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP294Sodium Formate, 4.4 M
Crystal Properties
Matthews coefficientSolvent content
3.1360.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 248.624α = 90
b = 110.355β = 129.63
c = 160.046γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.000ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.551.3499.20.9925.594225386
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6599.10.1

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 REPLACEMENTTHROUGHOUT5mns2.751.3487164438899.90.207210.204140.26804RANDOM65.582
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]
-1.27-0.231.84-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.317
r_dihedral_angle_3_deg19.137
r_dihedral_angle_4_deg18.388
r_long_range_B_refined7.741
r_long_range_B_other7.74
r_dihedral_angle_1_deg6.807
r_mcangle_it5.425
r_mcangle_other5.424
r_scangle_other5.036
r_mcbond_it3.348
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.317
r_dihedral_angle_3_deg19.137
r_dihedral_angle_4_deg18.388
r_long_range_B_refined7.741
r_long_range_B_other7.74
r_dihedral_angle_1_deg6.807
r_mcangle_it5.425
r_mcangle_other5.424
r_scangle_other5.036
r_mcbond_it3.348
r_mcbond_other3.348
r_scbond_it3.028
r_scbond_other3.026
r_angle_refined_deg1.524
r_angle_other_deg1.235
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
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 Atoms18627
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms438

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing