3A18 | pdb_00003a18

Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (soaked crystal)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A15	PDB ENTRY 3A15

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
2.2	44.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.118	α = 90
b = 148.569	β = 90.3
c = 79.113	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		2008-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	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	1.8	20	99.7	0.084	17.235	4.2		132895		-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	1.8	1.86	98		0.288		3.3	12998

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 3A15	1.8	19.93	132702	6625	98.82	0.249	0.247	0.25	0.28	0.28	RANDOM	11.456

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]
0.26			0.41		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.152
r_dihedral_angle_4_deg	16.825
r_dihedral_angle_3_deg	13.621
r_dihedral_angle_1_deg	5.904
r_scangle_it	1.408
r_angle_refined_deg	1.112
r_scbond_it	0.949
r_mcangle_it	0.666
r_mcbond_it	0.4
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.152
r_dihedral_angle_4_deg	16.825
r_dihedral_angle_3_deg	13.621
r_dihedral_angle_1_deg	5.904
r_scangle_it	1.408
r_angle_refined_deg	1.112
r_scbond_it	0.949
r_mcangle_it	0.666
r_mcbond_it	0.4
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.235
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11249
Nucleic Acid Atoms
Solvent Atoms	868
Heterogen Atoms	196

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SPACE	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.