2JI6 | pdb_00002ji6

X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP and oxalyl-CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C31	PDB ENTRY 2C31

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.9	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.002	α = 90
b = 127.002	β = 90
c = 151.813	γ = 120

Symmetry
Space Group	P 31 2 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	MARRESEARCH	VERTICALLY FOCUSING CYLINDRICAL MIRROR	2006-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711		MAX II	I711

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	2.06	152	96.2	0.1	11.8	6		84850			24.88

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	2.06	2.17	74.2		0.5	2.5	4.4

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 2C31	2.06	30	80775	3994	98.5	0.176	0.174	0.18	0.212	0.22	RANDOM	25.33

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]
2.91	1.46		2.91		-4.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.669
r_dihedral_angle_4_deg	15.752
r_dihedral_angle_3_deg	13.939
r_dihedral_angle_1_deg	5.761
r_scangle_it	1.897
r_scbond_it	1.486
r_angle_refined_deg	1.388
r_mcangle_it	1.323
r_mcbond_it	1.107
r_angle_other_deg	0.905
r_symmetry_vdw_other	0.248
r_nbd_refined	0.192
r_nbd_other	0.184
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.141
r_symmetry_vdw_refined	0.128
r_chiral_restr	0.119
r_nbtor_other	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8348
Nucleic Acid Atoms
Solvent Atoms	908
Heterogen Atoms	272

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing