X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Sodium Formate 4.4M
Crystal Properties
Matthews coefficientSolvent content
3.1160.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 247.758α = 90
b = 110.489β = 129.66
c = 159.818γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.000ELETTRA11.2C

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
11.9648.198.80.080.9977.343.4462764
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)
11.962.0897.80.3233

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 REPLACEMENTTHROUGHOUT5mns2.0848.03188451996399.80.173310.170370.22779RANDOM55.005
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]
-0.27-0.060.150.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.072
r_dihedral_angle_4_deg18.202
r_dihedral_angle_3_deg17.93
r_long_range_B_refined10.862
r_long_range_B_other10.862
r_scangle_other8.171
r_mcangle_it7.164
r_mcangle_other7.164
r_dihedral_angle_1_deg6.827
r_scbond_it6.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.072
r_dihedral_angle_4_deg18.202
r_dihedral_angle_3_deg17.93
r_long_range_B_refined10.862
r_long_range_B_other10.862
r_scangle_other8.171
r_mcangle_it7.164
r_mcangle_other7.164
r_dihedral_angle_1_deg6.827
r_scbond_it6.128
r_scbond_other6.128
r_mcbond_it5.496
r_mcbond_other5.496
r_angle_refined_deg1.857
r_angle_other_deg1.36
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.006
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 Atoms18686
Nucleic Acid Atoms
Solvent Atoms1339
Heterogen Atoms899

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing