X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6A7P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727732% PEG 3350, 50mM potassium phosphate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.346.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.998α = 90
b = 183.182β = 106.514
c = 59.175γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-12-02MSINGLE 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)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
12.995098.40.10412.446.224010
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.993.195.21.1141.525.5

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 REPLACEMENTFREE R-VALUE6A7P2.99248.23123776122297.9970.1990.19610.246182.163
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]
19.3315.16719.059-38.389
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.729
r_lrange_it18.407
r_dihedral_angle_3_deg15.029
r_mcangle_it13.892
r_scangle_it13.647
r_dihedral_angle_4_deg13.461
r_scbond_it9.897
r_mcbond_it9.524
r_dihedral_angle_1_deg4.833
r_angle_refined_deg1.234
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.729
r_lrange_it18.407
r_dihedral_angle_3_deg15.029
r_mcangle_it13.892
r_scangle_it13.647
r_dihedral_angle_4_deg13.461
r_scbond_it9.897
r_mcbond_it9.524
r_dihedral_angle_1_deg4.833
r_angle_refined_deg1.234
r_symmetry_nbd_refined0.333
r_nbtor_refined0.295
r_nbd_refined0.221
r_xyhbond_nbd_refined0.188
r_symmetry_xyhbond_nbd_refined0.1
r_chiral_restr0.069
r_bond_refined_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8337
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing