2HE4 | pdb_00002he4

The crystal structure of the second PDZ domain of human NHERF-2 (SLC9A3R2) interacting with a mode 1 PDZ binding motif

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I92	1i92 and 1g9o
experimental model	PDB	1G9O	1i92 and 1g9o

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.803	α = 90
b = 37.677	β = 97.7
c = 40.34	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	MARRESEARCH		2006-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97646	SLS	X10SA

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	1.45	39.97	98.5	0.0385		0.98	13265	13060

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)
	1.45	1.55	98		0.1403	6.45	0.98	2349

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	1i92 and 1g9o	1.45	39.97	13060	12418	641	98.46	0.13203	0.13203	0.12965	0.13	0.18003	0.18	RANDOM	14.015

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]
2.05		1.34	-1.13		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.109
r_dihedral_angle_4_deg	13.576
r_dihedral_angle_3_deg	10.62
r_sphericity_free	10.418
r_scangle_it	8.624
r_dihedral_angle_1_deg	6.535
r_scbond_it	6.273
r_sphericity_bonded	5.954
r_mcangle_it	4.686
r_mcbond_it	3.816
r_rigid_bond_restr	2.851
r_mcbond_other	2.47
r_angle_refined_deg	1.594
r_angle_other_deg	0.957
r_symmetry_vdw_other	0.29
r_symmetry_vdw_refined	0.248
r_symmetry_hbond_refined	0.231
r_nbd_refined	0.217
r_nbd_other	0.197
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.16
r_chiral_restr	0.094
r_nbtor_other	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	719
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing