2A13 | pdb_00002a13

X-ray structure of protein from Arabidopsis thaliana AT1G79260

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	10 MG/ML PROTEIN, 18% PEG2K, 0.025 M TRIS, pH 8.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.5
2.4	48.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.056	α = 90
b = 80.026	β = 90
c = 36.886	γ = 90

Symmetry
Space Group	P 21 21 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 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-06-13	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-06-13	M	MAD
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 22-ID	0.97934, 0.96863	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	1.31	50	96.3	0.066	14.91	7.5		41019

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)
	1.31	1.34	93.1	93.1	0.24	6.178	6.8

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 (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	MAD	THROUGHOUT	1.32	48.06	38582	2068	95.4	0.157	0.15708	0.156	0.1538	0.186	0.1842	RANDOM	17.287

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]
0.07			-0.1		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.693
r_dihedral_angle_4_deg	18.235
r_dihedral_angle_3_deg	11.941
r_dihedral_angle_1_deg	6.37
r_scangle_it	3.552
r_sphericity_free	3.111
r_sphericity_bonded	3.071
r_scbond_it	2.751
r_rigid_bond_restr	2.309
r_mcangle_it	1.834
r_mcbond_it	1.329
r_angle_refined_deg	1.311
r_nbtor_refined	0.292
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.179
r_symmetry_vdw_refined	0.16
r_symmetry_hbond_refined	0.109
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1220
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SOLOMON	phasing
ARP/wARP	model building