2PA1 | pdb_00002pa1

Structure of the PDZ domain of human PDLIM2 bound to a C-terminal extension from human beta-tropomyosin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		IN-HOUSE MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	294	30 % PEG Monomethylether 2000, 0.2M Ammonium sulfate, 0.1 M Sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.77	α = 90
b = 58.77	β = 90
c = 52.34	γ = 120

Symmetry
Space Group	P 61

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	MARMOSAIC 225 mm CCD		2007-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.95400	SLS	X10SA

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	1.7	50	99.7	0.056	18.1	6.2	11401	11401			31.4

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	1.7	1.8	98.5		0.532	1.88	3.4	1794

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	IN-HOUSE MODEL	1.7	29.39	11381	11381	544	99.83	0.195	0.195	0.192	0.19	0.253	0.25	RANDOM	32.275

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]
1.67	0.83		1.67		-2.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.649
r_dihedral_angle_4_deg	17.102
r_dihedral_angle_3_deg	13.718
r_dihedral_angle_1_deg	6.069
r_scangle_it	2.229
r_scbond_it	1.416
r_angle_refined_deg	1.199
r_mcangle_it	0.832
r_mcbond_it	0.601
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.649
r_dihedral_angle_4_deg	17.102
r_dihedral_angle_3_deg	13.718
r_dihedral_angle_1_deg	6.069
r_scangle_it	2.229
r_scbond_it	1.416
r_angle_refined_deg	1.199
r_mcangle_it	0.832
r_mcbond_it	0.601
r_nbtor_refined	0.294
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.176
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	639
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XDS	data scaling

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 R01GM157729.