9OWB | pdb_00009owb

Human WRN helicase in complex with allosteric ligand Compound 6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherproprietary model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27720.0% w/v PEG3350, 200 mM ammonium tartrate
Crystal Properties
Matthews coefficientSolvent content
2.2745.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.085α = 90.03
b = 58.394β = 90
c = 131.907γ = 90
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

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
11.55653.594.40.0360.99811.42.3234986
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)
11.5561.58366.60.4960.7341.32.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5653.46226751823594.410.151240.14970.16030.192340.1972RANDOM31.791
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]
1.780.01-0.030.45-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.246
r_dihedral_angle_4_deg15.39
r_dihedral_angle_3_deg12.189
r_dihedral_angle_1_deg6.443
r_long_range_B_refined4.028
r_long_range_B_other3.806
r_scangle_other2.986
r_mcangle_it2.869
r_mcangle_other2.869
r_rigid_bond_restr2.443
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.246
r_dihedral_angle_4_deg15.39
r_dihedral_angle_3_deg12.189
r_dihedral_angle_1_deg6.443
r_long_range_B_refined4.028
r_long_range_B_other3.806
r_scangle_other2.986
r_mcangle_it2.869
r_mcangle_other2.869
r_rigid_bond_restr2.443
r_scbond_it2.381
r_scbond_other2.381
r_mcbond_it2.198
r_mcbond_other2.196
r_angle_refined_deg1.331
r_angle_other_deg1.304
r_chiral_restr0.066
r_bond_other_d0.009
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13643
Nucleic Acid Atoms
Solvent Atoms1504
Heterogen Atoms297

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction