9MFT | pdb_00009mft

Human DHX9 in Complex with ATX968 and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8SZP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.2 M Lithium sulfate, 0.1 M MES pH 6.4, 20% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.8256.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.875α = 90
b = 85.875β = 90
c = 350.085γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2023-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.97918SSRFBL02U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.7554.321000.18915.624.935391
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.881001.6872.425.5

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 REPLACEMENTTHROUGHOUT2.7554.3233275180099.410.25270.249760.250.308730.3088RANDOM68.056
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]
0.530.53-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.066
r_dihedral_angle_3_deg13.886
r_dihedral_angle_4_deg13.157
r_long_range_B_refined5.505
r_long_range_B_other5.48
r_dihedral_angle_1_deg5.129
r_mcangle_it3.2
r_mcangle_other3.2
r_scangle_other2.563
r_mcbond_it1.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.066
r_dihedral_angle_3_deg13.886
r_dihedral_angle_4_deg13.157
r_long_range_B_refined5.505
r_long_range_B_other5.48
r_dihedral_angle_1_deg5.129
r_mcangle_it3.2
r_mcangle_other3.2
r_scangle_other2.563
r_mcbond_it1.813
r_mcbond_other1.813
r_scbond_it1.407
r_scbond_other1.403
r_angle_refined_deg1.169
r_angle_other_deg1.015
r_chiral_restr0.035
r_bond_refined_d0.002
r_gen_planes_refined0.002
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 Atoms6774
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms83

Software

Software
Software NamePurpose
Aimlessdata reduction
DIALSdata scaling
PHASERphasing
REFMACrefinement