X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L8G4l8g.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29332% PEG 4K 0.1M NaOAc (unbuffered) 8% 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
2.1241.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.918α = 90
b = 61.8β = 111.37
c = 76.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MOsmic confocal mirrors2017-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.943096.30.07615.86.4547734
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.941.9992.80.210.2350.1025.75.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4l8g.pdb1.9428.32146376237596.3180.1770.17460.22220.445
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]
-0.9210.595-0.1220.441
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.299
r_dihedral_angle_4_deg21.5
r_dihedral_angle_3_deg14.629
r_dihedral_angle_other_3_deg11.309
r_dihedral_angle_1_deg6.558
r_lrange_it5.186
r_lrange_other5.12
r_scangle_other3.595
r_scangle_it3.541
r_mcangle_it2.453
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.299
r_dihedral_angle_4_deg21.5
r_dihedral_angle_3_deg14.629
r_dihedral_angle_other_3_deg11.309
r_dihedral_angle_1_deg6.558
r_lrange_it5.186
r_lrange_other5.12
r_scangle_other3.595
r_scangle_it3.541
r_mcangle_it2.453
r_mcangle_other2.453
r_scbond_other2.279
r_scbond_it2.26
r_angle_refined_deg1.787
r_mcbond_it1.641
r_mcbond_other1.639
r_angle_other_deg1.36
r_nbd_other0.227
r_nbd_refined0.215
r_symmetry_nbd_refined0.202
r_symmetry_xyhbond_nbd_refined0.188
r_symmetry_nbd_other0.18
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.164
r_symmetry_nbtor_other0.077
r_chiral_restr0.072
r_metal_ion_refined0.018
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_xyhbond_nbd_other0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_xyhbond_nbd_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5413
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms288

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing