8ATJ

Crystal Structure of Shank2-SAM domain

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F44

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	0.1M Bis Tris pH5.5, 0.3M of Magnesium formate

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.49	α = 90
b = 57.49	β = 90
c = 48.033	γ = 120

Symmetry
Space Group	P 65

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 EIGER X 16M		2021-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9762	PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.1	49.8	99.92	0.2587	0.05916	0.996	10.07	19.8		5201

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	2.1	2.16	100		1.42	0.3268	0.568	1.61	19.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2F44	2.117	49.788	5122	247	98.085	0.198	0.1956	0.2517	38.747

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]
0.269	0.135		0.269		-0.873

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.586
r_dihedral_angle_4_deg	22.922
r_dihedral_angle_3_deg	14.627
r_lrange_it	7.996
r_lrange_other	7.996
r_dihedral_angle_1_deg	5.684
r_scangle_other	5.497
r_scangle_it	5.495
r_mcangle_it	3.774
r_mcangle_other	3.769
r_scbond_it	3.546
r_scbond_other	3.521
r_mcbond_it	2.641
r_mcbond_other	2.64
r_angle_refined_deg	1.488
r_angle_other_deg	1.22
r_xyhbond_nbd_refined	0.249
r_metal_ion_refined	0.249
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.214
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.15
r_nbd_other	0.125
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	570
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing