X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2944.2 M Sodium Formate (HCOONa)
Crystal Properties
Matthews coefficientSolvent content
3.160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 247.379α = 90
b = 111.149β = 129.4
c = 159.144γ = 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 11.2C1.00ELETTRA11.2C

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
11.965097.70.0640.9977.82.7462663
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)
11.962.081.640.362

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5MNS2.0848.09189127994399.730.174380.171680.22501RANDOM56.045
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]
-1.76-0.551.370.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.064
r_dihedral_angle_4_deg19.694
r_dihedral_angle_3_deg18.351
r_long_range_B_refined7.817
r_long_range_B_other7.796
r_dihedral_angle_1_deg6.804
r_scangle_other3.899
r_mcangle_it3.368
r_mcangle_other3.368
r_scbond_it2.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.064
r_dihedral_angle_4_deg19.694
r_dihedral_angle_3_deg18.351
r_long_range_B_refined7.817
r_long_range_B_other7.796
r_dihedral_angle_1_deg6.804
r_scangle_other3.899
r_mcangle_it3.368
r_mcangle_other3.368
r_scbond_it2.817
r_scbond_other2.519
r_mcbond_it2.291
r_mcbond_other2.291
r_angle_refined_deg1.754
r_angle_other_deg1.341
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.006
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 Atoms18570
Nucleic Acid Atoms
Solvent Atoms1159
Heterogen Atoms1173

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing