2OCS

The crystal structure of the first PDZ domain of human NHERF-2 (SLC9A3R2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel		swissmodel generated model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	20% PEG 3350, 0.20M KSCN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.556	α = 90
b = 39.867	β = 106.93
c = 37.278	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		2006-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		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	1.5	35.66	100	0.0656	0.05	12.68	3.67	12062	12057

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)
	1.5	1.6	100		0.4595	0.322	5.4	3.64	2093

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	swissmodel generated model	1.5	35.66	12062	11448	609	99.96	0.15411	0.15411	0.15185	0.19829	RANDOM	14.108

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]
-0.29		0.03	-0.63		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.583
r_dihedral_angle_4_deg	17.97
r_dihedral_angle_3_deg	12.38
r_sphericity_free	9.877
r_dihedral_angle_1_deg	6.303
r_scangle_it	6.052
r_sphericity_bonded	5.218
r_scbond_it	4.131
r_mcangle_it	3.173
r_mcbond_it	2.188
r_rigid_bond_restr	2.077
r_angle_refined_deg	1.941
r_angle_other_deg	1.222
r_mcbond_other	1.062
r_symmetry_vdw_refined	0.397
r_symmetry_vdw_other	0.382
r_chiral_restr	0.377
r_nbd_refined	0.276
r_nbd_other	0.235
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.177
r_symmetry_hbond_refined	0.161
r_nbtor_other	0.092
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.002
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	664
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	7

Software

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