X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP294Sodium Formate, 4.4M
Crystal Properties
Matthews coefficientSolvent content
3.1560.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 248.135α = 90
b = 111.117β = 129.67
c = 160.543γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C0.9788ELETTRA11.2C

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
12.4448.0798.20.0480.9913.553241832
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)
12.442.5996.70.5980.7471.81

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 REPLACEMENTTHROUGHOUT5mns2.4448.07117365599199.050.189880.187140.24333RANDOM60.212
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]
-2.82-1.112.450.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.999
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg18.249
r_long_range_B_refined9.129
r_long_range_B_other9.129
r_scangle_other6.866
r_dihedral_angle_1_deg6.794
r_mcangle_it6.676
r_mcangle_other6.675
r_scbond_it4.622
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.999
r_dihedral_angle_4_deg18.546
r_dihedral_angle_3_deg18.249
r_long_range_B_refined9.129
r_long_range_B_other9.129
r_scangle_other6.866
r_dihedral_angle_1_deg6.794
r_mcangle_it6.676
r_mcangle_other6.675
r_scbond_it4.622
r_mcbond_it4.605
r_mcbond_other4.604
r_scbond_other4.598
r_angle_refined_deg1.555
r_angle_other_deg1.213
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.004
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 Atoms18485
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms603

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing