9OWA | pdb_00009owa

Human WRN helicase in complex with allosteric ligand Compound 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherproprietary model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27723-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25
Crystal Properties
Matthews coefficientSolvent content
2.3247.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.06α = 90
b = 57.95β = 90
c = 132.39γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2023-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9838.976.80.9896.33.223910
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)
11.9842.01875.50.7490.7231.42.6

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 REPLACEMENTTHROUGHOUT1.9838.921476242976.710.259270.253940.25520.305610.3054RANDOM50.031
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]
1.95-2.370.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.354
r_dihedral_angle_4_deg15.813
r_dihedral_angle_3_deg13.949
r_dihedral_angle_1_deg7.132
r_long_range_B_refined3.782
r_long_range_B_other3.774
r_angle_refined_deg1.371
r_angle_other_deg1.099
r_mcangle_it0.999
r_mcangle_other0.999
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.354
r_dihedral_angle_4_deg15.813
r_dihedral_angle_3_deg13.949
r_dihedral_angle_1_deg7.132
r_long_range_B_refined3.782
r_long_range_B_other3.774
r_angle_refined_deg1.371
r_angle_other_deg1.099
r_mcangle_it0.999
r_mcangle_other0.999
r_scangle_other0.766
r_mcbond_it0.557
r_mcbond_other0.557
r_scbond_it0.439
r_scbond_other0.439
r_chiral_restr0.054
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3338
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms65

Software

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