32CR | pdb_000032cr

SHANK3 PDZ (570-664) in complex with an internal PDZ binding motif (843-864) in Densin-180

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292.15	60 mM magnesium chloride hexahydrate, 60 mM calcium chloride dihydrate, 100 mM Tris/Bicine pH 8.5, 12% v/v PEG 500 MME, 6% w/v PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.89	α = 90
b = 71.34	β = 90
c = 114.92	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	DECTRIS EIGER2 X 9M		2026-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.62	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.98	47.64	100	0.201	1	7.6	6.6		37309

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.01	99.8		1.804	0.4	1.1	5.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.98	47.639	37260	1727	99.89	0.204	0.201	0.2042	0.2566	0.2066	39.889

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]
-1.55			1.401		0.149

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.622
r_dihedral_angle_6_deg	15.499
r_lrange_it	9.291
r_lrange_other	9.272
r_dihedral_angle_2_deg	8.428
r_dihedral_angle_1_deg	6.644
r_scangle_it	6.543
r_scangle_other	6.542
r_mcangle_it	5.913
r_mcangle_other	5.912
r_scbond_it	4.322
r_scbond_other	4.32
r_mcbond_it	4.011
r_mcbond_other	4.01
r_angle_refined_deg	1.728
r_angle_other_deg	0.581
r_symmetry_nbd_refined	0.217
r_nbd_other	0.208
r_nbd_refined	0.206
r_symmetry_nbd_other	0.201
r_xyhbond_nbd_refined	0.2
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3524
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing