7YKI | pdb_00007yki

Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR3 peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	2.1 M ammonium phosphate dibasic, 0.2 M ammonium sulfate, 0.1M Tris (pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.975	α = 90
b = 78.909	β = 90
c = 92.997	γ = 90

Symmetry
Space Group	P 21 2 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	CCD	ADSC QUANTUM 315r		2013-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97930	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	50	97.3	0.091	12.9	4.3		32529

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	98.9		0.506		4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2EEH,5YPO	2	44.496	32474	1601	96.94	0.209	0.2074	0.22	0.2486	0.25	28.078

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]
4.342			-2.295		-2.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.143
r_dihedral_angle_3_deg	14.466
r_dihedral_angle_2_deg	12.674
r_lrange_it	8.682
r_lrange_other	8.578
r_dihedral_angle_1_deg	6.835
r_scangle_it	6.097
r_scangle_other	6.096
r_mcangle_it	4.329
r_mcangle_other	4.329
r_scbond_it	3.928
r_scbond_other	3.927
r_mcbond_it	2.887
r_mcbond_other	2.883
r_angle_refined_deg	1.489
r_angle_other_deg	0.496
r_xyhbond_nbd_refined	0.248
r_nbd_refined	0.217
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.178
r_nbd_other	0.178
r_symmetry_xyhbond_nbd_other	0.152
r_ncsr_local_group_2	0.147
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.131
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.067
r_ncsr_local_group_1	0.059
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	3006
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing