3CBY

The Dvl2 PDZ Domain in Complex with the N1 Inhibitory Peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	1.6 M tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.303	α = 90
b = 52.187	β = 100.33
c = 31.911	γ = 90

Symmetry
Space Group	C 1 2 1

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 315		2006-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	ALS	5.0.2

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	1.5	50	98.3	0.065	19.3	5.1		34942

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)
	1.5	1.55	96.8		0.636	2.6	4.9	3410

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3CBX	1.5	20	33035	1743	98.3	0.136	0.134	0.182	RANDOM	17.255

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]
-0.49		0.61	0.32		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.227
r_sphericity_free	14.781
r_dihedral_angle_3_deg	11.923
r_dihedral_angle_4_deg	10.478
r_scangle_it	7.804
r_sphericity_bonded	7.246
r_mcangle_it	6.34
r_scbond_it	5.941
r_dihedral_angle_1_deg	5.558
r_mcbond_it	5.219
r_rigid_bond_restr	3.252
r_mcbond_other	2.601
r_angle_refined_deg	1.513
r_angle_other_deg	0.915
r_symmetry_vdw_other	0.252
r_nbd_refined	0.216
r_xyhbond_nbd_refined	0.199
r_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_vdw_refined	0.136
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.09
r_nbtor_other	0.086
r_bond_refined_d	0.014
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	1559
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	8

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction