2FE5 | pdb_00002fe5

The Crystal Structure of the Second PDZ Domain of Human DLG3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BYG	2BYG.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	Ammonium sulphate, Glycerol, Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.487	α = 90
b = 40.242	β = 92.8
c = 33.34	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2005-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97910	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.1	26.45	98.4				27971

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16	96.6

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	2BYG.pdb	1.1	26.45	26547	26547	1406	98.11	0.11512	0.11512	0.11322	0.12	0.15038	0.11	RANDOM	7.076

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]
0.23		0.15	0.1		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.642
r_dihedral_angle_3_deg	12.6
r_dihedral_angle_4_deg	12.292
r_sphericity_free	8.369
r_dihedral_angle_1_deg	6.347
r_scangle_it	6.059
r_scbond_it	4.751
r_sphericity_bonded	4.091
r_mcangle_it	3.634
r_mcbond_it	3.211
r_rigid_bond_restr	2.087
r_mcbond_other	1.813
r_angle_refined_deg	1.439
r_angle_other_deg	0.873
r_symmetry_vdw_refined	0.304
r_symmetry_vdw_other	0.278
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.2
r_nbd_other	0.182
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.163
r_chiral_restr	0.09
r_nbtor_other	0.084
r_bond_refined_d	0.009
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	698
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing