9MFP | pdb_00009mfp

Cat DHX9 in Complex with Compound 1 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		293	0.15 M Ammonium sulfate, 0.1 M TRIS pH 8, 15% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.47	α = 90
b = 86.47	β = 90
c = 351.17	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 EIGER X 9M		2023-06-02	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)	CC (Half)	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	2.27	48.52	99.97	0.123	0.999	18.5	25.5		59824

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)	Redundancy	Number Unique Reflections (All)
1	2.27	2.329	99.91		1.616	0.766	2.4	27.4

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	2.27	48.52	59824	3088	99.97	0.19712	0.19465	0.1988	0.24593	0.2472	RANDOM	53.724

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]
0.04			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.905
r_dihedral_angle_4_deg	17.301
r_dihedral_angle_3_deg	14.482
r_long_range_B_refined	8.761
r_long_range_B_other	8.755
r_scangle_other	6.64
r_dihedral_angle_1_deg	6.554
r_mcangle_other	5.661
r_mcangle_it	5.66
r_scbond_it	4.313
r_scbond_other	4.312
r_mcbond_it	3.839
r_mcbond_other	3.832
r_angle_refined_deg	1.405
r_angle_other_deg	1.206
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
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	6799
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data processing
XDS	data scaling
PHASER	phasing
Coot	model building
Aimless	data reduction