8TYU

High-resolution crystal structure of the SPX domain of XPR1 at 1.4 angstroms

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	6% PEG 3350, 30% Ethylene Glycol, 0.1 M Sodium Citrate, 0.1 M MgCl2, pH 6.0.

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 47.798	β = 107.15
c = 71.682	γ = 90

Symmetry
Space Group	P 1 21 1

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 16M		2019-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	1.3	50	97.2	0.052	0.057	0.024	0.992	12.2	5.3		87185

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	1.3	1.32	80		0.62	0.69	0.292	0.876		3.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.4	35.75	66210	1802	94.58	0.16243	0.16166	0.19108	RANDOM	18.496

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]
2.07		0.02	-0.7		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.65
r_rigid_bond_restr	12.235
r_dihedral_angle_2_deg	5.906
r_long_range_B_refined	5.319
r_dihedral_angle_1_deg	5.279
r_long_range_B_other	5.106
r_mcbond_it	4.25
r_mcbond_other	4.244
r_scangle_other	4.134
r_mcangle_it	4.076
r_mcangle_other	4.075
r_scbond_it	3.392
r_scbond_other	3.392
r_angle_refined_deg	1.342
r_angle_other_deg	0.449
r_chiral_restr	0.069
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2867
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
REFMAC	phasing