3CBZ | pdb_00003cbz

The Dvl2 PDZ Domain in Complex with the N2 Inhibitory Peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CBX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	0.1 M HEPES, 0.8 M sodium phosphate, 0.8 M Potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.675	α = 90
b = 43.554	β = 90
c = 54.86	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	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	1.38	50	99.3	0.046	32.1	5.5		21576

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)
	1.38	1.43	94.6		0.397	2.8	4.3	2018

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3CBX	1.38	20	20391	1096	99.31	0.139	0.137	0.14	0.166	0.17	RANDOM	13.494

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]
-0.66			-0.17		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.528
r_dihedral_angle_4_deg	18.42
r_sphericity_free	16.502
r_dihedral_angle_3_deg	11.615
r_sphericity_bonded	8.475
r_scangle_it	7.228
r_dihedral_angle_1_deg	6.089
r_scbond_it	5.434
r_mcangle_it	5.38
r_mcbond_it	4.704
r_rigid_bond_restr	3.205
r_mcbond_other	2.942
r_angle_refined_deg	1.6
r_angle_other_deg	0.936
r_nbd_refined	0.208
r_nbd_other	0.193
r_symmetry_vdw_refined	0.191
r_xyhbond_nbd_refined	0.189
r_symmetry_vdw_other	0.184
r_nbtor_refined	0.174
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.103
r_nbtor_other	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	801
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	13

Software

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