3A15 | pdb_00003a15

Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (OxdRE)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	18% (W/V) PEG 4000, 0.075M sodium cacodylate, 0.1M magnesium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.904	α = 90
b = 77.066	β = 101.06
c = 104.831	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2008-02-06	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2008-02-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU
2	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.7379, 1.7404, 1.7200	SPring-8	BL41XU

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	1.79	20	99.6	0.057	22.83	4.4		141582		-3

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	1.79	1.86	98.7		0.325	2.6	2.8	13938

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 (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	1.79	19.88	141557	7085	98.89	0.163	0.161	0.1609	0.193	0.1921	RANDOM	29.25

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]
-0.09		-0.37	0.01		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.814
r_dihedral_angle_4_deg	18.255
r_dihedral_angle_3_deg	12.55
r_dihedral_angle_1_deg	6.006
r_scangle_it	2.487
r_scbond_it	1.6
r_angle_refined_deg	1.229
r_mcangle_it	1.033
r_mcbond_it	0.649
r_nbtor_refined	0.299
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.179
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11376
Nucleic Acid Atoms
Solvent Atoms	1299
Heterogen Atoms	172

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing