2Q27 | pdb_00002q27

Crystal structure of oxalyl-coA decarboxylase from Escherichia coli

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	281	1.5M ammonium sulfate, 0.0025M thiamine diphosphate, 0.0025 mM magnesium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.11	α = 90
b = 145.44	β = 90
c = 147.98	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		2006-12-06	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	2.12	99	99.8	0.107	10.7	7		80614

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)
	2.12	2.16	99.9		0.739		5.6	4002

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.12	18.31	78322	3939	97.16	0.195	0.193	0.237	0.2376	RANDOM	36.972

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.586
r_dihedral_angle_4_deg	19.121
r_dihedral_angle_3_deg	15.374
r_dihedral_angle_1_deg	6.36
r_scangle_it	4.438
r_scbond_it	2.982
r_angle_refined_deg	1.908
r_mcangle_it	1.779
r_mcbond_it	1.139
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.128
r_metal_ion_refined	0.038
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8234
Nucleic Acid Atoms
Solvent Atoms	433
Heterogen Atoms	131

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
HKL-2000	data scaling