2PNT | pdb_00002pnt

Crystal structure of the PDZ domain of human GRASP (GRP1) in complex with the C-terminal peptide of the metabotropic glutamate receptor type 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GQ4	PDB entries 1GQ4, 2OCS
experimental model	PDB	2OCS	PDB entries 1GQ4, 2OCS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	298	1.26M NaH2PO4, 0.14M K2HPO4, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.288	α = 90
b = 72.288	β = 90
c = 163.311	γ = 120

Symmetry
Space Group	P 65 2 2

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		2007-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.035	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	2.148	62.622	100	0.091		8.8	14546	14546

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.148	2.23	99.9			6.5	1411

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 1GQ4, 2OCS	2.148	62.62	13758	13758	729	99.91	0.20995	0.20995	0.20876	0.22	0.23198	0.24	RANDOM	34.719

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]
0.33	0.17		0.33		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.899
r_dihedral_angle_4_deg	23.675
r_dihedral_angle_3_deg	15.342
r_dihedral_angle_1_deg	7.072
r_scangle_it	3.934
r_scbond_it	2.54
r_mcangle_it	1.612
r_angle_refined_deg	1.517
r_angle_other_deg	0.923
r_mcbond_it	0.919
r_symmetry_vdw_refined	0.257
r_symmetry_vdw_other	0.255
r_symmetry_hbond_refined	0.226
r_mcbond_other	0.201
r_nbd_other	0.198
r_nbd_refined	0.197
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.097
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1414
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing