5QU8

Crystal Structure of symmetric swapped human Nck SH3.1 domain, 0.93A, orthorhombic form IV

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	60% tacsimate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.45	15.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.1	α = 90
b = 55.17	β = 90
c = 27	γ = 90

Symmetry
Space Group	P 21 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	PSI PILATUS 6M		2020-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00005	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	0.93	27.6	88.1	0.065	0.072	0.999	6.8	5.45		36162			17.679

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.93	1.06	63.6		14.779	17.331	0.17	3.539

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	inhouse model	0.93	27.6	18459	961	47.37	0.1506	0.1489	0.1821	RANDOM	17.542

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]
1.35			-1.77		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.761
r_dihedral_angle_4_deg	32.824
r_dihedral_angle_3_deg	13.159
r_dihedral_angle_1_deg	6.621
r_rigid_bond_restr	5.892
r_angle_refined_deg	1.842
r_angle_other_deg	1.44
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.761
r_dihedral_angle_4_deg	32.824
r_dihedral_angle_3_deg	13.159
r_dihedral_angle_1_deg	6.621
r_rigid_bond_restr	5.892
r_angle_refined_deg	1.842
r_angle_other_deg	1.44
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	493
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.