1XMB | pdb_00001xmb

X-ray structure of IAA-aminoacid hydrolase from Arabidopsis thaliana gene AT5G56660

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	10 mg/mL PROTEIN, 0.080 M MAGNESIUM SULFATE, 14 % PEG 1500, 0.100 M CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.264	α = 90
b = 75.264	β = 90
c = 130.88	γ = 120

Symmetry
Space Group	P 32 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	110	CCD	APS-1	Rosenbaum-Rock vertical focusing mirror	2004-08-01	M	SINGLE WAVELENGTH
2	1	x-ray	110	CCD	APS-1	Rosenbaum-Rock vertical focusing mirror	2004-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.96411	APS	19-BM
2	SYNCHROTRON	APS BEAMLINE 19-BM	0.97932	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	2	24.21	99.9	0.043	22	8.4		29672

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	2	2.07	99.9		0.334	3.8	6.3

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-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	24.21	29630	1504	99.821	0.159	0.159	0.1567	0.17	0.2039	0.22	RANDOM	27.747

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]
-0.005	-0.003		-0.005		0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.503
r_dihedral_angle_4_deg	20.747
r_dihedral_angle_3_deg	14.355
r_scangle_it	7.081
r_dihedral_angle_1_deg	6.279
r_scbond_it	5.454
r_scangle_other	3.065
r_mcangle_it	2.872
r_mcbond_it	2.193
r_scbond_other	1.828
r_angle_refined_deg	1.587
r_mcangle_other	1.339
r_angle_other_deg	0.838
r_mcbond_other	0.353
r_symmetry_vdw_other	0.279
r_symmetry_hbond_refined	0.261
r_xyhbond_nbd_refined	0.252
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.197
r_nbd_other	0.189
r_nbtor_refined	0.177
r_chiral_restr	0.099
r_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2889
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
ARP/wARP	model building
RESOLVE	phasing
REFMAC	refinement