2XTZ | pdb_00002xtz

Crystal structure of the G alpha protein AtGPA1 from Arabidopsis thaliana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FQJ	PDB ENTRY 1FQJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	CRYSTALS OF ATGPA1 WERE GROWN AT 4 DEGREES CELSIUS USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. DROPS CONTAINED 1.5 UL OF PROTEIN SOLUTION (20 MG/ML ATGPA1 IN 25 MM TRIS-HCL, PH 7.4, 5% (V/V) GLYCEROL, 150 MM SODIUM CHLORIDE, 1 MM DTT, 500 UL GTP-GAMMA-S) AND WERE EQUILIBRATED AGAINST 1.5 UL OF 0.3 M MAGNESIUM SULFATE, 0.1 M SODIUM CACODYLATE, PH 6.0, 21% (W/V) PEG 8000. INITIALLY OBTAINED CRYSTALS WERE USED FOR MACROSEEDING. CRYSTALS REACHED THEIR FINAL ROD-SHAPE FORM WITHIN 14 DAYS AFTER MACROSEEDING AND WERE CRYOPROTECTED IN THE MOTHER LIQUOR WITH 8% (V/V) GLYCEROL.

Crystal Properties
Matthews coefficient	Solvent content
2.6	53.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.13	α = 90
b = 119.347	β = 90
c = 161.725	γ = 90

Symmetry
Space Group	P 21 21 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 MX300	CUSTOM	2009-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	2.34	44.6	100	0.11	17.5	6		55808		-3	52.9

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	2.34	2.36	100		0.84	1.9	5.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FQJ	2.34	96.03	54216	1520	99.89	0.21247	0.2113	0.2	0.25378	0.25	RANDOM	44.512

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]
0.03			1.37		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.609
r_dihedral_angle_4_deg	19.857
r_dihedral_angle_3_deg	15.294
r_dihedral_angle_1_deg	5.256
r_scangle_it	2.368
r_scbond_it	1.473
r_angle_refined_deg	1.249
r_mcangle_it	0.802
r_mcbond_it	0.407
r_nbtor_refined	0.304
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.079
r_metal_ion_refined	0.043
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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	7505
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	128

Software

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