8S1R

Crystal structure of SHANK1 PDZ in complex with a SLiM internal ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YWZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20 % v/v ethylene glycol, 10 % w/v PEG 8000, 0.018 M magnesium chloride, 0.018 M calcium chloride, 0.1 M tris pH 7.5, 0.1 M bicine pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
4.01	69.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.101	α = 90
b = 149.101	β = 90
c = 64.066	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	100	PIXEL	DECTRIS EIGER2 X CdTe 9M		2022-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9999	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.979	129.125	100	0.123	0.039	0.999	14.7	20.7		57199			34.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.979	2.01			1.661	0.56	0.837	1.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.979	129.125	57178	3012	100	0.217	0.2158	0.2358	46.681

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]
0.787	0.393		0.787		-2.553

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.745
r_dihedral_angle_3_deg	13.313
r_dihedral_angle_4_deg	12.086
r_lrange_other	8.826
r_lrange_it	8.822
r_dihedral_angle_1_deg	6.681
r_scangle_it	6.273
r_scangle_other	6.273
r_mcangle_it	5.179
r_mcangle_other	5.178
r_scbond_it	3.949
r_scbond_other	3.949
r_mcbond_it	3.426
r_mcbond_other	3.426
r_angle_refined_deg	1.399
r_angle_other_deg	1.236
r_symmetry_xyhbond_nbd_refined	0.239
r_nbd_refined	0.184
r_symmetry_nbd_other	0.165
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.163
r_nbtor_refined	0.153
r_symmetry_nbd_refined	0.105
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3596
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DIALS	data reduction
PHASER	phasing
Coot	model building
REFMAC	refinement