8SZP | pdb_00008szp

Human DHX9 bound to ADP

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	200 mM Lithium sulfate, 100 mM MES pH 6, 20% (w/v) PEG 4000; 5 mM ADP and 50 mM magnesium chloride in protein solution

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.1	α = 90
b = 122.26	β = 90
c = 349.18	γ = 90

Symmetry
Space Group	C 2 2 21

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 XE 16M		2021-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97624	Diamond	I03

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	2.62	61.13	99.7	0.062	0.064	0.018	1	21.8	12.8		76541

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	2.62	2.67		99.4	1.398	1.45	0.382	0.815		14

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	2.62	59.621	76498	3769	99.552	0.222	0.2194	0.22	0.2736	0.27	RANDOM	87.946

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]
5.65			-3.047		-2.602

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.486
r_dihedral_angle_6_deg	12.623
r_lrange_other	9.925
r_lrange_it	9.924
r_mcangle_it	6.778
r_mcangle_other	6.778
r_scangle_it	6.631
r_scangle_other	6.631
r_dihedral_angle_1_deg	6.123
r_mcbond_it	4.251
r_mcbond_other	4.246
r_dihedral_angle_2_deg	4.177
r_scbond_it	4.014
r_scbond_other	4.014
r_angle_refined_deg	0.877
r_angle_other_deg	0.296
r_nbd_refined	0.203
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.144
r_nbd_other	0.109
r_symmetry_xyhbond_nbd_refined	0.081
r_symmetry_nbtor_other	0.073
r_symmetry_nbd_refined	0.067
r_symmetry_xyhbond_nbd_other	0.047
r_chiral_restr	0.042
r_chiral_restr_other	0.026
r_dihedral_angle_other_2_deg	0.012
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13583
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	165

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing