4PZG | pdb_00004pzg

Crystal structure of human sorting nexin 10 (SNX10)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	4 M sodium nitrate, 0.1 M BIS-TRIS propane pH 7.0, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
5.24	76.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 205.859	α = 90
b = 205.859	β = 90
c = 42.33	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315		2014-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9792	SSRF	BL17U

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	2.8	49.45	98.7	0.136	10.5	6.5		25144

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	2.8	2.95	94.6		0.674	2.2	3.8	3465

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	49.45	25133	1277	98.7	0.1966	0.1944	0.237	0.2115	RANDOM	42.045

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]
1.14	1.14		1.14		-3.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.47
r_dihedral_angle_4_deg	21.886
r_dihedral_angle_3_deg	19.942
r_dihedral_angle_1_deg	7.387
r_angle_refined_deg	1.97
r_angle_other_deg	1.255
r_chiral_restr	0.102
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2558
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	87

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction