X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29315-20% PEG3350, 0.1M Tris-HCl pH 8-8.5, 0.3M Li2SO4, 0-10% ethylene glycol, Microseed matrix screening
Crystal Properties
Matthews coefficientSolvent content
2.2445.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.507α = 108.208
b = 69.069β = 92.088
c = 90.993γ = 106.747
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.72738DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.9744.194.40.1160.1640.1160.9946.63.868392
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.011.5572.21.5540.273.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9744.168300326694.6440.2020.19960.241838.744
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]
0.475-0.48-1.0140.5070.172-0.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.255
r_dihedral_angle_3_deg14.72
r_dihedral_angle_2_deg13.407
r_dihedral_angle_1_deg7.351
r_lrange_it6.435
r_lrange_other6.424
r_scangle_it4.219
r_scangle_other4.196
r_mcangle_it3.796
r_mcangle_other3.795
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.255
r_dihedral_angle_3_deg14.72
r_dihedral_angle_2_deg13.407
r_dihedral_angle_1_deg7.351
r_lrange_it6.435
r_lrange_other6.424
r_scangle_it4.219
r_scangle_other4.196
r_mcangle_it3.796
r_mcangle_other3.795
r_scbond_it2.748
r_scbond_other2.732
r_mcbond_it2.458
r_mcbond_other2.458
r_angle_refined_deg2.139
r_angle_other_deg0.746
r_xyhbond_nbd_refined0.315
r_symmetry_xyhbond_nbd_refined0.252
r_nbd_refined0.226
r_symmetry_nbd_refined0.194
r_nbtor_refined0.178
r_symmetry_nbd_other0.177
r_nbd_other0.171
r_ncsr_local_group_10.108
r_chiral_restr0.106
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_other0.08
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8018
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing