X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829330% (w/v) polyethylene glycol 10000, 0.2 M MgCl2, 0.1 M Na K tartrate, 0.1 M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
1.7429.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.891α = 90
b = 80.9β = 90
c = 92.661γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
12.246.399.80.1250.0540.9929.66.420772
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2399.70.3380.140.9354.8

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 REPLACEMENTTHROUGHOUT1W182.244.320660101199.2980.2240.22170.265728.338
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]
-0.0060.014-0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.734
r_dihedral_angle_3_deg15.42
r_dihedral_angle_4_deg13.269
r_dihedral_angle_1_deg8.058
r_lrange_it5.293
r_lrange_other5.288
r_scangle_it3.815
r_scangle_other3.814
r_mcangle_it3.269
r_mcangle_other3.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.734
r_dihedral_angle_3_deg15.42
r_dihedral_angle_4_deg13.269
r_dihedral_angle_1_deg8.058
r_lrange_it5.293
r_lrange_other5.288
r_scangle_it3.815
r_scangle_other3.814
r_mcangle_it3.269
r_mcangle_other3.269
r_scbond_it2.601
r_scbond_other2.601
r_angle_other_deg2.41
r_mcbond_it2.233
r_mcbond_other2.231
r_angle_refined_deg1.636
r_symmetry_nbd_refined0.286
r_nbd_other0.271
r_symmetry_xyhbond_nbd_refined0.242
r_symmetry_nbd_other0.217
r_nbd_refined0.202
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.16
r_metal_ion_refined0.149
r_symmetry_xyhbond_nbd_other0.077
r_symmetry_nbtor_other0.076
r_chiral_restr0.069
r_bond_other_d0.036
r_gen_planes_other0.011
r_bond_refined_d0.009
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3694
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing