2Q28 | pdb_00002q28

Crystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with adenosine-5`-diphosphate

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	281	1.75M ammonium sulfate, 0.005M adenosine diphosphate, 0.0025M thiamine diphosphate, 0.0025 mM magnesium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.27	α = 90
b = 143.62	β = 90
c = 147.58	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		2006-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.93001	EMBL/DESY, HAMBURG	X12

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	1.74	99	99.9	0.104	8.5	7.2		143107

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)
	1.74	1.77	100		0.867		6.8	7085

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	1.74	20.61	142512	1436	99.61	0.178	0.177	0.177	0.196	0.1922	RANDOM	20.11

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	38.269
r_dihedral_angle_4_deg	14.294
r_dihedral_angle_3_deg	12.541
r_dihedral_angle_1_deg	5.571
r_scangle_it	3.272
r_scbond_it	2.052
r_angle_refined_deg	1.397
r_mcangle_it	1.184
r_mcbond_it	0.742
r_nbtor_refined	0.306
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8294
Nucleic Acid Atoms
Solvent Atoms	892
Heterogen Atoms	158

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