3B76 | pdb_00003b76

Crystal structure of the third PDZ domain of human ligand-of-numb protein-X (LNX1) in complex with the C-terminal peptide from the coxsackievirus and adenovirus receptor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AWW	PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L
experimental model	PDB	2BYG	PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L
experimental model	PDB	2AWX	PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L
experimental model	PDB	2AWU	PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L
experimental model	PDB	2G2L	PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	1.53M Potassium phosphate, 0.27M Sodium phosphate, 1% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.782	α = 90
b = 58.449	β = 90
c = 73.741	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	MARMOSAIC 225 mm CCD		2007-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99975	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.75	33.71	100	0.094	0.094	16	7.2	22359	22359			20.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.84	100		0.844	0.844	2.9	7.3	23287

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	PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L	1.75	33.71	21214	21214	1144	99.92	0.17657	0.17657	0.175	0.18	0.20529	0.21	RANDOM	17.652

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]
0.56			-0.88		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.772
r_dihedral_angle_3_deg	11.648
r_scangle_it	10.02
r_dihedral_angle_4_deg	9.689
r_scbond_it	7.164
r_dihedral_angle_1_deg	5.877
r_mcangle_it	5.194
r_mcbond_it	3.711
r_angle_other_deg	1.913
r_mcbond_other	1.566
r_angle_refined_deg	1.404
r_symmetry_vdw_other	0.315
r_symmetry_vdw_refined	0.207
r_nbd_other	0.196
r_nbd_refined	0.188
r_symmetry_hbond_refined	0.169
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.088
r_nbtor_other	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1513
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing