8SZS | pdb_00008szs

Cat DHX9 bound to GDP

X-RAY DIFFRACTION

---

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	8.2	291	0.15 M ammonium sulfate, 0.1 M Tris, pH 8.2, 15% w/v PEG4000; 5 mM GDP and 50 mM magnesium chloride in protein solution

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.11	α = 90
b = 86.11	β = 90
c = 347.24	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 PILATUS3 6M		2021-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.38	48.03	100	0.144	0.147	0.029	0.999	17.4	26.1		53722

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)	Redundancy	Number Unique Reflections (All)
1	2.38	2.45		100	1.542	1.575	0.317	0.834		24.2

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 (All)	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	2.38	48.03	53717	2726	99.97	0.22	0.2176	0.22	0.2646	0.27	RANDOM	51.881

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]
0.496			0.496		-0.992

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.277
r_dihedral_angle_3_deg	11.949
r_lrange_it	6.105
r_lrange_other	6.093
r_dihedral_angle_1_deg	5.62
r_scangle_it	3.51
r_scangle_other	3.51
r_mcangle_it	3.126
r_mcangle_other	3.126
r_dihedral_angle_2_deg	3.044
r_scbond_it	2.017
r_scbond_other	2.017
r_mcbond_it	1.868
r_mcbond_other	1.867
r_angle_refined_deg	0.792
r_angle_other_deg	0.269
r_symmetry_xyhbond_nbd_refined	0.192
r_nbd_refined	0.191
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.17
r_nbd_other	0.153
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.072
r_symmetry_nbd_refined	0.06
r_chiral_restr	0.039
r_dihedral_angle_other_2_deg	0.012
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6787
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	142

Software

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