3SOE

Crystal Structure of the 3rd PDZ domain of the human Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3 (MAGI3)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BPU	Ensemble of 3BPU, 2R4H, 2Q9V
experimental model	PDB	2R4H	Ensemble of 3BPU, 2R4H, 2Q9V
experimental model	PDB	2Q9V	Ensemble of 3BPU, 2R4H, 2Q9V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1M Bis-tris pH 6.0 0.25M Li2SO4 35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.63	α = 90
b = 59.28	β = 90
c = 65.35	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	IMAGE PLATE	RIGAKU RAXIS IV		2011-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.52

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	22.52	97.9	0.046	0.046	17.1	4.7	18521	18132			23.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.68	95		0.515	0.515	1.5	3.8	2491

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of 3BPU, 2R4H, 2Q9V	1.6	22.52	18532	18095	924	97.64	0.1894	0.1894	0.188	0.2164	RANDOM	23.4798

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]
			1.14		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.489
r_dihedral_angle_4_deg	20.595
r_dihedral_angle_3_deg	12.033
r_scangle_it	6.467
r_dihedral_angle_1_deg	5.469
r_scbond_it	4.211
r_mcangle_it	2.74
r_mcbond_it	1.576
r_angle_refined_deg	1.403
r_angle_other_deg	0.887

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.489
r_dihedral_angle_4_deg	20.595
r_dihedral_angle_3_deg	12.033
r_scangle_it	6.467
r_dihedral_angle_1_deg	5.469
r_scbond_it	4.211
r_mcangle_it	2.74
r_mcbond_it	1.576
r_angle_refined_deg	1.403
r_angle_other_deg	0.887
r_mcbond_other	0.449
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	765
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.