2JIL

Crystal structure of 2nd PDZ domain of glutamate receptor interacting protein-1 (GRIP1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N7E	PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F
experimental model	PDB	1TQ3	PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F
experimental model	PDB	1BE9	PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F
experimental model	PDB	1MFG	PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F
experimental model	PDB	2HE2	PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F
experimental model	PDB	1N7F	PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		20% PEG3350, 0.20M POTASSIUM THIOCYANATE, 10% ETHYLENE GLYCOL, 0.1M BIS TRIS PROPANE PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.98	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.06	α = 90
b = 61.057	β = 90
c = 96.397	γ = 90

Symmetry
Space Group	C 2 2 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	MARRESEARCH		2007-05-10	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)	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	41.31	99.9	0.06	16	4.2		26857			21.03

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	1.5	1.58	99.7		0.56	1.6	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F	1.5	48.22	24603	2226	99.8	0.192	0.189	0.228	RANDOM	17.94

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]
0.89			0.19		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.306
r_dihedral_angle_4_deg	20.649
r_dihedral_angle_3_deg	13.705
r_scangle_it	8.437
r_scbond_it	6.146
r_dihedral_angle_1_deg	5.92
r_mcangle_it	4.035
r_mcbond_it	2.646
r_angle_other_deg	1.678
r_angle_refined_deg	1.519
r_symmetry_vdw_other	0.377
r_symmetry_vdw_refined	0.367
r_nbd_refined	0.264
r_nbd_other	0.228
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.139
r_nbtor_other	0.087
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.004
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1411
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	18

Software

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