9D5Z | pdb_00009d5z

Crystal structure of the human WDR5 in complex with LH168 compound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SMR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29120% PEG3350, 0.2 M Ammonium formate
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.951α = 110.41
b = 61.185β = 91.22
c = 64.605γ = 112.2
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2024-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.18049CLSI08B1-1

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
11.75094.10.0460.0550.0290.9948.33.463599
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)
11.71.7380.60.3160.3760.20.9363.2

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 REPLACEMENTTHROUGHOUT1.742.8962385121293.930.140330.13940.15060.188720.19RANDOM22.816
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]
0.06-0.25-0.911.880.31-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined12.649
r_dihedral_angle_3_deg11.541
r_long_range_B_other11.381
r_dihedral_angle_1_deg8.353
r_scangle_other6.921
r_mcangle_it6.527
r_mcangle_other6.527
r_dihedral_angle_2_deg5.241
r_scbond_it4.589
r_scbond_other4.589
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined12.649
r_dihedral_angle_3_deg11.541
r_long_range_B_other11.381
r_dihedral_angle_1_deg8.353
r_scangle_other6.921
r_mcangle_it6.527
r_mcangle_other6.527
r_dihedral_angle_2_deg5.241
r_scbond_it4.589
r_scbond_other4.589
r_mcbond_it4.28
r_mcbond_other4.272
r_rigid_bond_restr2.24
r_angle_refined_deg1.305
r_angle_other_deg0.475
r_chiral_restr0.065
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms4711
Nucleic Acid Atoms
Solvent Atoms474
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PHASERphasing