1YDH | pdb_00001ydh

X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	293	10 MG/ML PROTEIN, 13% MPEG 2K, 0.28 M POTASSIUM NITRATE, 0.1 M MOPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.589	α = 90
b = 80.427	β = 102.97
c = 50.709	γ = 90

Symmetry
Space Group	C 1 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	CCD	APS-1	SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR	2004-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	2.152	35.451	99.9	0.384	6.266	6.9		25771

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)
	2.15	2.23	100		0.384	2.401	6.2

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	SAD	THROUGHOUT	2.152	35.45	25679	1300	99.1	0.16164	0.16164	0.159	0.1843	0.213	0.2302	RANDOM	31.14

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]
0.915		0.386	-0.158		-0.584

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.733
r_dihedral_angle_4_deg	21.845
r_dihedral_angle_3_deg	14.836
r_scangle_it	6.985
r_dihedral_angle_1_deg	5.547
r_scbond_it	5.121
r_mcangle_it	2.656
r_angle_refined_deg	1.939
r_mcbond_it	1.579
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.271
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.199
r_symmetry_hbond_refined	0.17
r_chiral_restr	0.112
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
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_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2798
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	20

Software

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