2A33 | pdb_00002a33

X-Ray Structure of a Lysine Decarboxylase-Like Protein from Arabidopsis Thaliana Gene AT2G37210

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	296	10 MG/ML PROTEIN, 22% PEG 2K, 0.084 M MAGNESIUM SULFATE, 0.100 M BISTRIS, vapor diffusion, hanging drop, temperature 296K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
1.9	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.403	α = 90
b = 66.773	β = 90
c = 98.639	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	MARMOSAIC 225 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM		APS	22-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	1.95	50	99.8	0.1	15.009	10.7		26424

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)
	1.95	2.02	98.6		0.518	1.756	4.8

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 1YDH	1.95	46.984	25025	1336	99.8	0.183	0.181	0.19	0.234	0.24	RANDOM	29.22

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]
-0.34			-0.31		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.466
r_dihedral_angle_4_deg	19.02
r_dihedral_angle_3_deg	15.764
r_scangle_it	7.146
r_dihedral_angle_1_deg	6.324
r_scbond_it	5.342
r_mcangle_it	2.946
r_mcbond_it	1.861
r_angle_refined_deg	1.712
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.271
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.135
r_symmetry_hbond_refined	0.126
r_metal_ion_refined	0.026
r_bond_refined_d	0.021
r_gen_planes_refined	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2636
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	11

Software

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