X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7T8P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727742% sodium polyacrylate 2100 0.05 M HEPES-NaOH pH 7
Crystal Properties
Matthews coefficientSolvent content
2.856.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.888α = 90
b = 100.888β = 90
c = 448.169γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.0150.1399.90.1520.99812.7710.1177907
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.1399.72.3770.413

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 SYNTHESISTHROUGHOUT2.0150.13170141776699.910.168570.167490.19136RANDOM37.947
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]
0.310.160.31-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg15.735
r_dihedral_angle_3_deg13.03
r_dihedral_angle_1_deg7.345
r_long_range_B_refined7.149
r_long_range_B_other7.135
r_scangle_other5.135
r_dihedral_angle_2_deg3.7
r_mcangle_other3.346
r_mcangle_it3.344
r_scbond_it3.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg15.735
r_dihedral_angle_3_deg13.03
r_dihedral_angle_1_deg7.345
r_long_range_B_refined7.149
r_long_range_B_other7.135
r_scangle_other5.135
r_dihedral_angle_2_deg3.7
r_mcangle_other3.346
r_mcangle_it3.344
r_scbond_it3.23
r_scbond_other3.23
r_mcbond_it2.301
r_mcbond_other2.301
r_angle_refined_deg1.069
r_angle_other_deg0.372
r_chiral_restr0.053
r_gen_planes_refined0.005
r_bond_refined_d0.004
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 Atoms15942
Nucleic Acid Atoms
Solvent Atoms2001
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing