6SPZ

Crystal structure of PDZ1-2 from PSD-95 with peptide ligand sequence RRESEI bound to both domains

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	0.2 M NaCl, 0.1 M Na/K phosphate, 50% v/v PEG 200. Matrix microseeding with Apo crystal form (PDB ID: 6spv).

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.5	α = 90
b = 50.5	β = 90
c = 176.37	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M		2014-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.979	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.08	48.55	100	0.075	0.998	14.5	7		13236

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.13	99.9		0.538	0.762	2.7	3.8

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	3rl7, 3rl8	2.08	48.549	13216	703	99.97	0.203	0.2004	0.2399	47.492

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]
0.226			0.226		-0.451

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.267
r_dihedral_angle_3_deg	12.131
r_dihedral_angle_4_deg	11.77
r_lrange_it	7.328
r_dihedral_angle_1_deg	5.46
r_scangle_it	3.253
r_mcangle_it	3.072
r_scbond_it	1.941
r_mcbond_it	1.754
r_angle_refined_deg	1.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.267
r_dihedral_angle_3_deg	12.131
r_dihedral_angle_4_deg	11.77
r_lrange_it	7.328
r_dihedral_angle_1_deg	5.46
r_scangle_it	3.253
r_mcangle_it	3.072
r_scbond_it	1.941
r_mcbond_it	1.754
r_angle_refined_deg	1.139
r_nbtor_refined	0.296
r_nbd_refined	0.19
r_symmetry_nbd_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.153
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.095
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1526
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
SCALA	data scaling
pointless	data scaling
PHASER	phasing

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.