2JI7 | pdb_00002ji7

X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate

X-RAY DIFFRACTION

---

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	57.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.181	α = 90
b = 126.181	β = 90
c = 151.938	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	ADSC CCD	TOROIDAL MIRROR	2006-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	76	99.2	0.09	10.2	3.7		124184			18.66

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	1.82	1.92	99.9		0.48	2	3.7

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	1.82	30	118269	5831	99.1	0.151	0.15	0.16	0.176	0.18	RANDOM	19.91

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]
1.17	0.59		1.17		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.749
r_dihedral_angle_4_deg	16.262
r_dihedral_angle_3_deg	12.422
r_dihedral_angle_1_deg	5.641
r_scangle_it	1.824
r_angle_other_deg	1.622
r_angle_refined_deg	1.425
r_scbond_it	1.222
r_mcangle_it	1.086
r_mcbond_it	0.804
r_symmetry_vdw_other	0.27
r_nbd_refined	0.2
r_nbd_other	0.181
r_nbtor_refined	0.167
r_symmetry_hbond_refined	0.162
r_chiral_restr	0.138
r_symmetry_vdw_refined	0.135
r_xyhbond_nbd_refined	0.118
r_nbtor_other	0.085
r_bond_other_d	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	1185
Heterogen Atoms	342

Software

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