2Q29 | pdb_00002q29

Crystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with acetyl coenzyme A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	281	6% PEG4000, 0.2M sodium acetate. 0.0025M thiamine diphosphate, 0.0025M magnesium sulfate, 0.001M acetyl coenzyme A, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.57	α = 90
b = 145.53	β = 90
c = 147.19	γ = 90

Symmetry
Space Group	C 2 2 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	MAR CCD 225 mm		2007-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9785	EMBL/DESY, HAMBURG	BW7A

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	1.82	99	100	0.052	14.6	7.2		126889

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)
	1.82	1.85	99.9		0.257		6.7	6263

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.82	42.3	126549	1275	99.76	0.175	0.175	0.17	0.194	0.19	RANDOM	19.584

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.611
r_dihedral_angle_4_deg	15.454
r_dihedral_angle_3_deg	12.434
r_dihedral_angle_1_deg	5.684
r_scangle_it	3.549
r_scbond_it	2.207
r_angle_refined_deg	1.443
r_mcangle_it	1.261
r_mcbond_it	0.826
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.611
r_dihedral_angle_4_deg	15.454
r_dihedral_angle_3_deg	12.434
r_dihedral_angle_1_deg	5.684
r_scangle_it	3.549
r_scbond_it	2.207
r_angle_refined_deg	1.443
r_mcangle_it	1.261
r_mcbond_it	0.826
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.21
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_metal_ion_refined	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8236
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms	140

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction

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.