5QU5 | pdb_00005qu5

Domain Swap in the first SH3 domain of human Nck1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		inhouse model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	5-20 mg/mL protein in 25mM HEPES\/NaOH pH7.8, 150mM NaCl mixed 60-70% with 40-30% reservoir consisting of 0.1M Bis-Tris/HCl pH5.5, 2M NaCl, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.2	α = 90
b = 55.17	β = 90
c = 55.23	γ = 90

Symmetry
Space Group	P 21 21 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	PSI PILATUS 6M		2018-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99994	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	1.1	39.03	96.4	0.077	0.083	0.999	8.16	7.215		48767			21.685

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	1.1	1.13	92.2		13.661	14.734	0.1	7.101

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	1.11	39.03	26973	1391	57.16	0.1551	0.1523	0.1529	0.2079	0.2088	RANDOM	20.141

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]
-0.48			0.22		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.387
r_dihedral_angle_4_deg	26.293
r_sphericity_free	25.637
r_dihedral_angle_3_deg	15.321
r_sphericity_bonded	12.21
r_dihedral_angle_1_deg	6.95
r_rigid_bond_restr	3.717
r_angle_refined_deg	2.037
r_angle_other_deg	1.084
r_chiral_restr	0.15
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1004
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	7

Software

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