1YBM | pdb_00001ybm

X-ray structure of selenomethionyl gene product from Arabidopsis thaliana at5g02240 in space group P21212

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	10 MG/ML PROTEIN, 24 PERCENT PEG 4K, 0.136 M SODIUM MALONATE, 0.10 M BISTRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.634	α = 90
b = 77.286	β = 90
c = 92.864	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	MAR CCD 165 mm	bent cylindrical Si-mirror (Rh coating)	2004-08-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.97935, 0.97904, 0.96389	APS	14-ID-B

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	2.096	29.087	93	0.047	22.745	11.7		29937

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)
	2.1	2.15	88.3		0.28	6.125	9.3

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.096	29.09	29855	1525	92.634	0.193	0.1888	0.19	0.2615	0.26	RANDOM	38.303

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]
-1.539			1.589		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.884
r_dihedral_angle_4_deg	15.382
r_dihedral_angle_3_deg	15.086
r_scangle_it	8.126
r_dihedral_angle_1_deg	6.592
r_scbond_it	6.383
r_mcangle_it	4.412
r_mcbond_it	3.22
r_angle_refined_deg	1.643
r_symmetry_hbond_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.884
r_dihedral_angle_4_deg	15.382
r_dihedral_angle_3_deg	15.086
r_scangle_it	8.126
r_dihedral_angle_1_deg	6.592
r_scbond_it	6.383
r_mcangle_it	4.412
r_mcbond_it	3.22
r_angle_refined_deg	1.643
r_symmetry_hbond_refined	0.306
r_nbtor_refined	0.299
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_refined	0.179
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3672
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	96

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.