6G8Y | pdb_00006g8y

Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	3.0 M NaCl, 100 mM Bis-Tris, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.443	α = 90
b = 53.443	β = 90
c = 50.923	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS PILATUS3 6M		2011-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.4	35	99.7	0.042	0.999	22.96	6.5		16914

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.44	99.7		0.74	0.84	2.82	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	SAD	THROUGHOUT	1.4	26.72	16072	846	99.68	0.16519	0.16285	0.16	0.21006	0.21	RANDOM	25.042

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]
-0.17	-0.09		-0.17		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.467
r_sphericity_free	21.033
r_dihedral_angle_3_deg	13.323
r_dihedral_angle_4_deg	12.059
r_sphericity_bonded	8.012
r_dihedral_angle_1_deg	6.028
r_long_range_B_refined	5.525
r_long_range_B_other	5.523
r_scangle_other	2.793
r_mcangle_it	2.707
r_mcangle_other	2.704
r_scbond_it	2.478
r_scbond_other	2.478
r_mcbond_other	2.294
r_mcbond_it	2.291
r_rigid_bond_restr	1.882
r_angle_refined_deg	1.452
r_angle_other_deg	0.985
r_chiral_restr	0.095
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	760
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Auto-Rickshaw	phasing