X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MDG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82911.6 M sodium citrate, 50 mM Tris-H2SO4
Crystal Properties
Matthews coefficientSolvent content
2.0840.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.15α = 90
b = 41.34β = 104.44
c = 72.35γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.0935.692.40.0510.060.99910.933.8419325215.822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.091.16790.9311.0840.531.183.731

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 SYNTHESISTHROUGHOUT4MDG1.135.689695183193.380.14350.14310.1656RANDOM17.428
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]
0.12-0.21-0.090.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.932
r_dihedral_angle_4_deg26.052
r_sphericity_free16.992
r_dihedral_angle_3_deg10.905
r_sphericity_bonded9.042
r_dihedral_angle_1_deg6.663
r_rigid_bond_restr4.542
r_angle_refined_deg1.635
r_angle_other_deg1.537
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.932
r_dihedral_angle_4_deg26.052
r_sphericity_free16.992
r_dihedral_angle_3_deg10.905
r_sphericity_bonded9.042
r_dihedral_angle_1_deg6.663
r_rigid_bond_restr4.542
r_angle_refined_deg1.635
r_angle_other_deg1.537
r_chiral_restr0.111
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2035
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
FFTphasing