9MFQ | pdb_00009mfq

Cat DHX9 in Complex with Compound 10 and ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8SZQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.15 M Ammonium sulfate, 0.1 M TRIS pH 8, 20% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.73	α = 90
b = 85.73	β = 90
c = 348.48	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 S 9M		2023-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.99	43.05	99.9	0.168	17.9	24.2		27613

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.99	3.17	99.6		1.186	2.9	19.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.99	42.9	26157	1357	99.78	0.22872	0.2262	0.2237	0.27682	0.2748	RANDOM	74.333

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]
1.7			1.7		-3.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.963
r_dihedral_angle_3_deg	13.689
r_dihedral_angle_4_deg	11.561
r_long_range_B_refined	5.339
r_long_range_B_other	5.307
r_dihedral_angle_1_deg	5.063
r_mcangle_it	3.193
r_mcangle_other	3.193
r_scangle_other	2.742
r_mcbond_it	1.841
r_mcbond_other	1.837
r_scbond_it	1.526
r_scbond_other	1.526
r_angle_refined_deg	1.159
r_angle_other_deg	1.012
r_chiral_restr	0.034
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	6793
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	98

Software

Software
Software Name	Purpose
Aimless	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement