X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52931 ul protein (10 mg/ml, 20 mM TRIS pH 7.5, 150 mM NaCl) + 1 ul reservoir (0.1 M sodium citrate or sodium acetate pH 5.0, 15% (v/v) PEG8000, 0.5 M lithium sulfate)
Crystal Properties
Matthews coefficientSolvent content
2.3347.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.121α = 90
b = 78.769β = 92.56
c = 140.121γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirror2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9799PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1210097.10.1310.1510.9918.44.27309027.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1295.30.7190.8380.621.63.6

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 REPLACEMENTTHROUGHOUT4CG1248.7369684360797.430.215780.213470.26091RANDOM23.386
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]
1.30.33-2.110.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.802
r_dihedral_angle_4_deg17.402
r_dihedral_angle_3_deg13.874
r_dihedral_angle_1_deg7.406
r_long_range_B_refined4.467
r_long_range_B_other4.401
r_angle_refined_deg1.817
r_angle_other_deg1.052
r_scangle_other0.826
r_mcangle_it0.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.802
r_dihedral_angle_4_deg17.402
r_dihedral_angle_3_deg13.874
r_dihedral_angle_1_deg7.406
r_long_range_B_refined4.467
r_long_range_B_other4.401
r_angle_refined_deg1.817
r_angle_other_deg1.052
r_scangle_other0.826
r_mcangle_it0.658
r_mcangle_other0.658
r_scbond_it0.587
r_scbond_other0.517
r_mcbond_it0.385
r_mcbond_other0.385
r_chiral_restr0.086
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms7689
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing